Abstracts of papers presented

at the 2019 meeting on

PLANT GENOMES, SYSTEMS

BIOLOGY & ENGINEERING
December 4–December 7, 2019
 Abstracts of papers presented
at the 2019 meeting on

PLANT GENOMES, SYSTEMS

BIOLOGY & ENGINEERING
December 4–December 7, 2019

Arranged by

Zach Lippman, Cold Spring Harbor Laboratory

Jane Parker, Max Planck Institute for Plant Breeding Research,
Germany
Sue Rhee, Carnegie Institution for Science
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____________________________________________________________

Cover image by Dmitry Lapin and Britta Hoffmann, Max-Planck Institute for
Plant Breeding Research, Cologne, Germany.
 PLANT GENOMES, SYSTEMS BIOLOGY & ENGINEERING
Wednesday, December 4 – Saturday, December 7, 2019

Wednesday 7:30 pm Keynote Speaker

Wednesday 8:15 pm 1 Crop Biology and Trait Enhancement

Thursday 9:00 am 2 Genomes and Epigenomes

Thursday 2:00 pm 3 Biodiversity and Environmental

Adaptation

Thursday 4:30 pm 4 Poster Session / Wine & Cheese Party

Thursday 7:30 pm 5 Plants and Microbes

Friday 9:00 am 6 Metabolic Circuits

Friday 2:00 pm 7 Development: Modules to Networks

Friday 5:00 pm Keynote Speaker

Friday 6:00 pm Banquet

Saturday 9:00 am 8 Frontier Technologies and Synthetic

Biology

Mealtimes at Blackford Hall are as follows:

Breakfast 7:30 am-9:00 am
Lunch 11:30 am-1:30 pm
Dinner 5:30 pm-7:00 pm

Bar is open from 5:00 pm until late

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respectful environment for all meeting attendees, and does not permit or
tolerate discrimination or harassment in any form. By participating in this
meeting, you agree to abide by the Code of Conduct, which is available
both online and at the back of this book.

___________________________________________________________

Abstracts are the responsibility of the author(s) and publication of an

abstract does not imply endorsement by Cold Spring Harbor Laboratory of
the studies reported in the abstract.

These abstracts should not be cited in bibliographies. Material herein

should be treated as personal communications and should be cited as
such only with the consent of the author(s).

Please note that photography or video/audio recording of oral

presentations or individual posters is strictly prohibited except with the
advance permission of the author(s), the organizers, and Cold Spring
Harbor Laboratory.

Any discussion via social media platforms of material presented at this

meeting requires explicit permission from the presenting author(s).

Printed on 100% recycled paper.

 PROGRAM

WEDNESDAY, December 4—7:30 PM

KEYNOTE SPEAKER

Introduction by: Jane Parker, Max-Planck Institute for Plant Breeding

Research

Epistasis, the spice of life—Lessons from the study of the plant

immune system
Detlef Weigel.
Presenter affiliation: Max Planck Institute for Developmental Biology,
Tübingen, Germany. 1

WEDNESDAY, December 4—8:15 PM

SESSION 1 CROP BIOLOGY AND TRAIT ENHANCEMENT

Chairperson: John Vogel, DOE Joint Genome Institute, Walnut Creek,

California

Gradual polyploid genome evolution revealed by a pan-genomic

analysis of Brachypodium hybridum and its diploid progenitors
Sean Gordon, Bruno Contreras-Moreira, Joshua Levy, Armin Djamei,
Angelika Czedik-Eysenberg, Virginia Tartaglio, Adam Session, Joel
Martin, Amy Cartwright, Andrew Katz, Vasanth Singan, Eugene
Goltsman, Kerrie Barry, Vinh Ha Dinh-Thi, Boulos Chalhoub, Antonio
Diaz-Perez, Ruben Sancho, Joanna Lusinska, Elzbieta Wolny,
Candida Nibau, John Doonan, Luis Mur, Chris Plott, Jerry Jenkins,
Samuel Hazen, Scott Lee, Shenquaing Shu, David Goodstein, Daniel
Rokhsar, Jeremy Schmutz, Robert Hasterok, Pilar Catalan, John
Vogel.
Presenter affiliation: DOE Joint Genome Institute, Walnut Creek,
California; University of California-Berkeley, Berkeley, California. 2

Towards mechanistic understanding of homoeolog expression

levels in polyploid wheat
Philippa Borrill, Ricardo Ramírez-González, Cristobal Uauy.
Presenter affiliation: University of Birmingham, Birmingham, United
Kingdom. 3

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RNA virus evasion of nonsense mediated decay
Anne E. Simon, Jared P. May.
Presenter affiliation: University of Maryland, College Park, Maryland. 4

Fertility of pedicellate spikelets in sorghum is controlled by a

jasmonic acid regulatory module
Nicholas Gladman, Yinping Jiao, Young Koung Lee, Lifang Zhang,
Ratan Chopra, Michael Regulski, Gloria Burow, Chad Hayes, Shawn
Christensen, Lavanya Dampanaboina, Junping Chen, John Burke,
Doreen Ware, Zhanguo Xin.
Presenter affiliation: Agricultural Research Service, Lubbock, Texas;
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. 5

Genomics of sorghum local adaptation to a parasitic plant

Jesse Lasky.
Presenter affiliation: Pennsylvania State University, University Park,
Pennsylvania. 6

THURSDAY, December 5—9:00 AM

SESSION 2 GENOMES AND EPIGENOMES

Chairperson: Mary Gehring, Whitehead Institute for Biomedical

Research, Cambridge, Massachusetts

Epigenetic processes at the single cell level—Analysis of

Arabidopsis imprinting dynamics
Mary Gehring.
Presenter affiliation: Whitehead Institute, Cambridge, Massachusetts. 7

Natural diversity in highly variable plant NLR immune receptors

Ksenia V. Krasileva.
Presenter affiliation: University of California, Berkeley, Berkeley,
California. 8

Identifying chromatin-accessible regions that actively drive gene

expression
Michael Dorrity, Cris Alexandre, Christine Queitsch, Josh T. Cuperus.
Presenter affiliation: University of Washington, Seattle, Washington. 9

vi
What limits meiotic recombination?
Raphael Mercier.
Presenter affiliation: Max Planck Institute for Plant Breeding Research,
Cologne, Germany; INRA, Versailles, France. 10

Widespread long-range Cis-regulatory elements in the maize

genome
William A. Ricci, Zefu Lu, Lexiang Ji, Alex P. Marand, Robert J.
Schmitz, Xiaoyu Zhang.
Presenter affiliation: University of Georgia, Athens, Georgia. 11

The A. thalianamethylome influences chromatin accessibility after

heat stress
Thanvi Srikant, Wei Yuan, Anjar Wibowo, Kenneth Berendzen, Katrin
Fritschi, Grey Monroe, Detlef Weigel.
Presenter affiliation: Max Planck Institute for Developmental Biology,
Tuebingen, Germany. 12

THURSDAY, December 5—2:00 PM

SESSION 3 BIODIVERSITY AND ENVIRONMENTAL ADAPTATION

Chairperson: Ute Krämer, Ruhr University Bochum, Germany

Adaptation to local soil composition in Arabidopsis halleri

Gwonjin Lee, Julia Q. Gonzalez, Justin Anderson, Bjoern Pietzenuk,
Ute Kraemer.
Presenter affiliation: Ruhr University Bochum, Bochum, Germany. 13

Protein and gene regulatory network involved in hormone-

dependent nutrient sensing
Benoit Lacombe.
Presenter affiliation: CNRS, Montpellier, France. 14

Structural variation in the LRR-RLK gene family drives receptor

diversification
Jarrett A. Man, Joseph P. Gallagher, Madelaine E. Bartlett.
Presenter affiliation: University of Massachusetts Amherst, Amherst,
Massachusetts. 15

Natural variation of gene regulatory networks

Arthur Korte, Jan Freudenthal, Ammarah Anwar, William Lopez.
Presenter affiliation: University of Wuerzburg, Wuerzburg, Germany. 16

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Spatial genetics of plant communities
Meredith C. Schuman, Ewa Czyz, Cheng Li, Felix Morsdorf, Kentaro K.
Shimizu, Bernhard Schmid, Michael E. Schaepman.
Presenter affiliation: University of Zurich, Zurich, Switzerland; Max
Planck Institute for Chemical Ecology, Jena, Germany. 17

THURSDAY, December 5—4:30 PM

SESSION 4 POSTER SESSION and WINE & CHEESE PARTY

Gene prediction and cycling behavior in Spirodela polyrhiza

using full-length cDNA sequencing over diel cycles
Bradley W. Abramson, Nolan Hartwick, Todd Michael.
Presenter affiliation: J. Craig Venter Institute, La Jolla, California. 18

Cell-type specific omics identifies spatiotemporal regulation of

plant development and plasticity under individual and abiotic
stress combinations
Amir H. Ahkami, Vimal K. Balasubramanian, Maria D. Rubio Wilhelmi,
Samuel Purvine, Lye Meng Markillie, Ying Zhu, Yongil Yong, Neal
Stewart, Stephen DiFazio, Eduardo Blumwald.
Presenter affiliation: Pacific Northwest National Laboratory (PNNL),
Richland, Washington. 19

The fragrant trait (2-acetyl-1-pyrroline)—A common survival

metabolite from crops to tree plants
Siwaret Arikit, Samart Wanchana, Apichart Vanavichit.
Presenter affiliation: Kasetsart University, Nakhon Pathom, Thailand. 20

A dynamic modeling approach to understand the links between

metal uptake and antibiotic resistance in plants
Mentewab Ayalew, Bethany Mwaura, Catherine Rono, Carla Kumbale,
Eberhard Voit.
Presenter affiliation: Spelman College, Atlanta, Georgia. 21

Expression patterns of DNA methyltransferases and

demethylases throughout plant growth and development and in
response to phytohormones
Morgan Bennett, Kailyn Cleaves, Tarek Hewezi.
Presenter affiliation: University of Tennessee, Knoxville, Tennessee. 22

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Species-specific duplication event controlling adaptive benefits in
Sorghum bicolor is only discoverable after improvement in
reference genome quality
Zachary W. Brenton, Elizabeth A. Cooper, Erin L. Connolly, Stephen
Kresovich.
Presenter affiliation: Clemson University, Clemson, South Carolina. 23

Characterizing genetic and transcript variation using long single

molecule sequencing in maize
Kapeel Chougule, Sharon Weix, Yinping Jiao, Bo Wang, Jianing Liu,
Arun Seetharam, Shujun Qu, Brett Hannigan, Chai Fungtammasan,
Victor Llaca, Kevin Fengler, Candice Hirsch, Matthew Hufford, Kelly
Dawe, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 24

Integration of multiple proteomics methods reveals the signaling

landscape of the AMPK ortholog SnRK1 in plants
Jelle Van Leene, Astrid Gadeyne, Chao Han, Dominique Eeckhout,
Caroline Matthijs, Nancy De Winne, Geert Persiau, Eveline Van De
Slijke, Geert De Jaeger.
Presenter affiliation: Ghent University, Ghent, Belgium; VIB, Ghent,
Belgium. 25

Transcriptome analysis of sugarcane genotypes contrasting for

biomass production
Augusto L. Diniz, Iago Maiochi, Monalisa S. Carneiro, Doreen Ware,
Glaucia M. Souza.
Presenter affiliation: University of São Paulo, São Paulo, Brazil; Cold
Spring Harbor Laboratory, Cold Spring Harbor, New York. 26

Identifying novel DNA-transcription factor interactions using

DAP-seq
Christina L. Ethridge, Kitra L. Cates, Nathalie G. Murphy, Zefu Lu,
Robert J. Schmitz.
Presenter affiliation: University of Georgia, Athens, Georgia. 27

Evolution and function of duplicate transcription factor genes

GT1 and VRS1 in maize and Brachypodium distachyon
Joseph P. Gallagher, Harry R. Klein, María Jazmín Abraham Juárez,
Madelaine E. Bartlett.
Presenter affiliation: University of Massachusetts, Amherst,
Massachusetts. 28

ix
Cis-regulatory architecture reveals potential regulatory circuits
involved in the transcriptional regulation of BiP genes in potato
Venura Herath, Mathieu Gayral, Nirakar Adhikari, Rita Miller,
Jeanmarie Verchot.
Presenter affiliation: Texas A&M University, College Station, Texas. 29

Rediscovery and functional characterization of the CaMV 35S

enhancer using STARR-seq
Tobias Jores, Christine Queitsch, Josh T. Cuperus, Stanley Fields.
Presenter affiliation: University of Washington, Seattle, Washington. 30

Reimagining how putrescine functions as a signaling

compound—The essential role of synthesis, compartmentation,
and transport
Kumud Joshi, Menaka Ariyaratne, Sheaza Ahmed, Andrea Kalinoski,
Paul F. Morris.
Presenter affiliation: Bowling Green State University, Bowling Green,
Ohio. 31

Understanding the epigenetic basis of plant nitrogen response

Russell S. Julian, Somaiah T. Balekuttira, Shoban K. Vimalarani,
Kranthi Varala, Ying Li.
Presenter affiliation: Purdue University, West Lafayette, Indiana. 32

Machine learning method towards genomic selection

Joseph K. Kawash, Nicholi Vorsa, Jennifer Johnson-Cicalese, James
J. Polashock.
Presenter affiliation: ORISE, Chatsworth, New Jersey; USDA-ARS,
Chatsworth, New Jersey. 33

URI mediates iron deficiency signaling in Arabidopsis thaliana

Sun A Kim, Ian S. LaCroix, Scott A. Gerber, Mary Lou Guerinot.
Presenter affiliation: Dartmouth College, Hanover, New Hampshire. 34

The role of aquaporins in water balance and nitrogen

sequestering
Per O. Kjellbom.
Presenter affiliation: Lund University, Lund, Sweden. 35

Sugar signalling interacts with transcriptional regulation to

suppress growth in maize carpels
Harry Klein, Maria Juarez, Michelle Heeney, Edgar Demesa-Arevalo,
Xiaosa Xu, Clinton Whipple, David Jackson, Madelaine Bartlett.
Presenter affiliation: University of Massachusetts Amherst, Amherst,
Massachusetts. 36

x
Advancing systems biology of plants—Transcriptomics and
genome-scale metabolic modeling using open-science
community platform of KBase
Vivek Kumar, Sunita Kumari, Doreen Ware, Sam Seaver, Christopher
Henry, Bob Cottingham, Adam Arkin.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 37

Variation in transcription factor—DNA interaction in natural

populations of Arabidopsis
Miaomiao Li, Nathaniel Angeles, Shao-shan Carol Huang.
Presenter affiliation: New York University, New York, New York. 38

Development of single nuclei -omic technologies to better

understand the transcriptional regulation of plant genes
Andrew Farmer, Sandra Thibivilliers, Ravneet Kaur, Marc Libault.
Presenter affiliation: University of Nebraska-Lincoln, Lincoln,
Nebraska. 39

Systems genetics analysis of waterlogging tolerance

mechanisms in Brassica
Jheng-Yang Ou, Po-Xing Zheng, Chen-Yu Lin, Yao-Cheng Lin.
Presenter affiliation: Academia Sinica, Tainan, Taiwan. 40

Molecular basis of variation in flowering behaviour in

Scandinavian population of perennial Arabis alpina
Yi-Chen Lin, Ulla Kemi, George Coupland.
Presenter affiliation: Max Planck Institute for Plant Breeding Research,
Cologne, Germany. 41

SciApps.org—A cloud-based platform for shareable and

reproducible bioinformatics workflows
Zhenyuan Lu, Liya Wang, Peter Van Buren, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 42

Natural and engineered alleles of FLM and FLC modulate

flowering time in Arabidopsis thaliana in a continuous and broad
phenotypic range
Ulrich Lutz, Claus Schwechheimer, Detlef Weigel.
Presenter affiliation: Max Planck Institute for Developmental Biology,
Tuebingen, Germany. 43

xi
Dissecting the gene regulatory network controlling phenolic
biosynthesis in maize using transcription factor mutants
Erika Magnusson, Peng Zhou, Peter Hermanson, Yi-Hsuan Chu, Lina
Gomez, Andrea Doseff, Natalia De Leon, John Gray, Candice Hirsch,
Erich Grotewold, Nathan Springer.
Presenter affiliation: University of Minnesota, St. Paul, Minnesota. 44

Double triage to identify poorly annotated genes in maize

Cristina F. Marco, Marcela K. Tello-Ruiz, Fei-Man Hsu, Rajdeep S.
Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael
Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C.
Barone, Cornel Ghiban, Demitri Muna, Andrew Olson, Liya Liya,
Doreen Ware, David A. Micklos.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 45

Post-genetic responses to phosphate starvation and heat stress

in Arabidopsis thaliana
Devang Mehta, Luc Cornet, Syed S. Ali, Maria Rodriguez, Matthias
Hirsch-Hoffmann, Mina Ghahrehmani, María Pérez-Fernández,
William C. Plaxton, Hervé Vanderschuren, R. Glen Uhrig.
Presenter affiliation: University of Alberta, Edmonton, Canada. 46

Annotation of the TUB transcription gene family in Zea mays

Sendi Meja, Marcela Karey Tello-Ruiz, Cristina Fernandez-Marco,
Doreen Ware, Christos Noutsos.
Presenter affiliation: SUNY College Old Westbury, Old Westbury, New
York; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. 47

Identification of lncRNAs by utilization of histone modification

data in Zea mays
John P. Mendieta, William A. Ricci, Robert J. Schmitz.
Presenter affiliation: University of Georgia, Athens, Georgia. 48

A transporter for delivering Zn to the developing tiller bud in rice

Shuai Mu, Mary L. Guerinot, Luqing Zheng.
Presenter affiliation: Nanjing Agricultural University, Nanjing, China;
Dartmouth College, Hanover, New Hampshire. 49

Characterization of the genome structure of an essential oil plant,

lavender (Lavandula angustifolia)
Radesh Nattamai Malli Pooranachandhiran, Calvin Sjaarda, Robert
Baldwin, Soheil Mahmoud, Ping Liang.
Presenter affiliation: Brock University, St.Catharines, Canada. 50

xii
Identification of a role for GmKIX1 in regulating organ size in
soybean
Cuong X. Nguyen, Kyle J. Paddock, Zhanyuan Zhang, Minviluz G.
Stacey.
Presenter affiliation: University of Missouri-Columbia, Columbia,
Missouri. 51

RNA Pol4 mediates divergent maternal and paternal impacts on

the Arabidopsis endosperm
Satyaki P. RV, Mary Gehring.
Presenter affiliation: Whitehead Institute for Biomedical Research,
Cambridge, Massachusetts. 52

Genome-wide association mapping and characterization of

candidate genes controlling dirty panicle disease resistance
Kanamon Riangwong, Theerayut Toojinda, Samart Wanchana,
Meechai Siangliw, Siwaret Arikit, Jintana Unartngam.
Presenter affiliation: Graduate School, Kasetsart Uniersity, Bangkok,
Thailand. 53

The Ve-resistance locus in tomato, a plant signalling intercept

Jane Robb, Hakeem O. Shittu, Christian D. Castroverde, Xin Xu,
Alexander Kurosky, Ross N. Nazar.
Presenter affiliation: University of Guelph, Guelph, Canada. 54

Diversity of MYB transcription factors across apple, grape and

kiwifruit genomes
Jessica A. Rodrigues, Richard V. Espley, Andrew C. Allan.
Presenter affiliation: New Zealand Institute for Plant & Food Research
Ltd, Auckland, New Zealand. 55

Distinct evolutionary origins of intron retention splicing events in

NHX1 antiporter transcripts relate to sequence specific
distinctions in Oryza species
Gothandapani Sellamuthu, Vidya Jegadeeson, Radha S. Sajeevan,
Raja Rajakani, Pavithra Parthasarathy, Lana Shabala, Zhong-Hua
Chen, Meixue Zhou, R Sowdhamini, Sergey Shabala, Gayatri
Venkataraman.
Presenter affiliation: M.S. Swaminathan Research Foundation,
Chennai, India. 56

xiii
Transgenic tobacco plants as a tool for correct hydroxylation and
synthesis of human collagen peptides
Yana Sindarovska, Maksym Vasylenko, Mykola Kuchuk.
Presenter affiliation: Institute of Cell Biology and Genetic Engineering
NASU, Kyiv, Ukraine. 57

young vs younger—bZIP transcription factor networks at two

developmental stages
Liang Song, Milad Alizadeh.
Presenter affiliation: University of British Columbia, Vancouver,
Canada. 58

Gene regulatory networks and chromatin regulation in control of

shoot architecture
Jazmine Humphreys, Stephanie Kerr, Christopher Ray, Christine
Beveridge, Milos Tanurdzic.
Presenter affiliation: The University of Queensland, St Lucia, Australia. 59

Gramene Knowledgebase—A unifying resources for comparative

genomics and pathway analysis
Marcela K. Tello-Ruiz, Sharon Wei, Andrew Olson, Justin Preece,
Sushma Naithani, Parul Gupta, Yinping Jiao, Bo Wang, Kapeel
Chougule, Vivek Kumar, Sunita Kumari, Peter D'Eustachio, Bruno
Contreras-Moreira, Irene Papatheodorou, Pankaj Jaiswal, Doreen
Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 60

CRISPR/Cas9 gene editing of soybean KAS1 alters seed

composition traits and plant growth
Kamaldeep S. Virdi, Madison Spencer, Adrian O. Stec, Ryan Merry,
Aaron J. Lorenz, Robert M. Stupar, Gary J. Muehlbauer.
Presenter affiliation: University of Minnesota, Saint Paul, Minnesota. 61

Variant phasing and haplotypic expression from single-molecule

long-read sequencing in maize
Bo Wang, Elizabeth Tseng, Primo Baybayan, Kevin Eng, Michael
Regulski, Yinping Jiao, Liya Wang, Andrew Olson, Kapeel Chougule,
Peter Van Buren, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 62

xiv
Access to MaizeCODE data via SciApps.org
Liya Wang, Zhenyuan Lu, Xiaofei Wang, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 63

Gramene subsites—Pangenome browsers for crops

Sharon Wei, Andrew Olson, Marcela K. Tello-Ruiz, Joshua Stein,
Kapeel Chougule, Yinping Jiao, Bo Wang, Ivar Meijs, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 64

Validation of genetic introgression by intersubgeneric

hybridization between Glycine max and Glycine tomentella
Lucas B. Santos, Joao P. Viana, Wei Wei, Xing Wu, Anete P. Souza,
Matthew Hudson, Steven J. Clough.
Presenter affiliation: University of Illinois, Urbana, Illinois. 65

Naturally occurring variation in an epigenetic control mechanism

Ben P. Williams, Drew Cohen, Mary Gehring.
Presenter affiliation: Whitehead Institute for Biomedical Research,
Cambridge, Massachusetts. 66

Insect herbivory elicits flower development gene networks as

induced defense in tomato leaves
Lanlan Ke, Yangzi Wang, Thomas Städler, Yuanyuan Song, Renseng
Zeng, Shuqing Xu.
Presenter affiliation: University of Münster, Münster, Germany. 67

Molecular characterization of Arabinoxylan fibers in oat

Jose A. Zambrano, Olof Olsson.
Presenter affiliation: Lund University, Lund, Sweden. 68

High-resolution expression quantitative trait nucleotide (eQTN)

mapping elucidates transcriptional regulation in Populus
trichocarpa
Jin Zhang, Jeremy Schmutz, Gerald Tuskan, Wellington Muchero, Jin-
Gui Chen.
Presenter affiliation: Oak Ridge National Laboratory, Oak Ridge,
Tennessee. 69

Characterizing key regulators of primary root development

Lifang Zhang, Andrew Olson, Fangle Hu, Allison Gaudinier, Siobhan
Brady, Doreen Ware.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Habor, New York. 70

xv
Maintenance of heterochromatin causes natural epigenetic
variation in Arabidopsis thaliana
Yinwen Zhang, Jered M. Wendte, Lexiang Ji, Bob Schmitz.
Presenter affiliation: University of Georgia, Athens, Georgia. 71

Building a computational framework of cell type-specific C4 plant

multiscale modeling to enhance biomass production under
drought in Sorghum
Cheng Zhao, Pascal Schläpfer, Edward J. Wolfrum, Jennifer Barrett,
Allen Hubbard, Hui Jiang, Xiaoping Li, Erica Agnew, Todd Mockler,
Ivan Baxter, Sue Rhee.
Presenter affiliation: Carnegie Institution for Science, Stanford,
California. 72

Delineating tissue- and condition- specific transcriptional

regulation of metabolism Arabidopsis thaliana
Kangmei Zhao, Michael Banf, Pascal Schläpfer, Sue Rhee.
Presenter affiliation: Carnegie Institution for Science, Palo Alto,
California. 73

Quantitative and genome-wide analysis of a transcription factor

module integrating light- and hormone-signaling pathways in
Arabidopsis
Jia-Ying Zhu, Zhi-Yong Wang.
Presenter affiliation: Carnegie Institution for Science, Stanford,
California. 74

THURSDAY, December 5—7:30 PM

SESSION 5 PLANTS AND MICROBES

Chairperson: Jian-Min Zhou, Institute of Genetics and Developmental

Biology, Chinese Academy of Sciences, Beijing, China

A plant secondary metabolite modifies bacterial transcription

factor to inhibit virulence
Jian-Min Zhou.
Presenter affiliation: Institute of Genetics and Developmental Biology,
Chinese Academy of Sciences, Beijing, China. 75

Lotus japonicus and rhizobia interactions; from simple to

complex associations
Simona Radutoiu.
Presenter affiliation: Aarhus University, Aarhus, Denmark. 76

xvi
Synthesis of indole-3 acetic acid by aphid saliva
Leila Feiz, Navid Movahed, Georg Jander.
Presenter affiliation: Boyce Thompson Institute, Ithaca, New York. 77

Functional genomics of rhizosphere-associated Pseudomonas

Cara H. Haney.
Presenter affiliation: The University of British Columbia, Vancouver,
Canada. 78

Resistance-related diversity in cereals response to pathogen

infection
Anna Piasecka, Aneta Sawikowska, Natalia Witaszak, Agnieszka
Waskiewicz, Joanna Kaczmarek.
Presenter affiliation: Institute of Plant Genetic of the Polish Academy of
Sciences, Poznan, Poland, Poznan, Poland; Institute of Bioorganic
Chemistry of the Polish Academy of Sciences, Poznan, Poland. 79

Functionally antagonistic integrated domains of the Rpg5 NLR

immunity receptor interact to regulate stem rust resistance in
barley
Shyam Solanki, Gazala Ameen, Deepika Arora, Pawel P. Borowicz,
Robert S. Brueggeman.
Presenter affiliation: Washington State University, Pullman,
Washington; NDSU, Fargo, North Dakota. 80

FRIDAY, December 6—9:00 AM

SESSION 6 METABOLIC CIRCUITS

Chairperson: Donald Ort, University of Illinois, Urbana, Illinois

Improving photosynthetic efficiency for improved crop yield

Paul F. South, Amanda P. Cavanagh, Donald R. Ort.
Presenter affiliation: University of Illinois, Urbana, Illinois. 81

Discovery and engineering of plant chemistry for plant and

human health
Elizabeth Sattely.
Presenter affiliation: Stanford University and HHMI, Stanford,
California. 82

xvii
Identification and characterization of novel regulators of low-
energy-signaling by SnRK1 in Arabidopsis thaliana
Jennifer Bortlik, Frederik Börnke.
Presenter affiliation: Leibniz-Institute Grossbeeren, Grossbeeren,
Germany; University of Potsdam, Potsdam, Germany. 83

Biosynthesis of cardiac glycosides in wallflowers (Erysimum,

Brassicaceae)
Tobias Züst, Susan R. Stickler, Adrian F. Powell, Mackenzie E. Mabry,
Hong An, Mahdieh Mirzaei, Thomas York, Cynthia K. Holland, Pavan
Kumar, Matthias Erb, Georg Petschenka, José María Goméz,
Francisco Perfectti, Caroline Müller, Chris Pires, Lukas A. Mueller,
Georg Jander.
Presenter affiliation: Boyce Thompson Institute, Ithaca, New York. 84

Reconstructing plant metabolism with synthetic biology

Patrick M. Shih.
Presenter affiliation: Patrick Shih, Davis, California. 85

Understanding cellular metabolism using systems engineering

approaches
Jin Wang.
Presenter affiliation: Auburn University, Auburn, Alabama. 86

FRIDAY, December 6—2:00 PM

SESSION 7 DEVELOPMENT: MODULES TO NETWORKS

Chairperson: Miriam Gifford, University of Warwick, Coventry,

United Kingdom

Timing and coordination of cell type response mechanisms that

regulate nodulation
Miriam L. Gifford, Beatriz Lagunas, Mingkee Achom, Chrysa Sergaki,
Liam Walker, Bethany L. Richmond, Proyash Roy, Patrick Schäfer.
Presenter affiliation: The University of Warwick, Coventry, United
Kingdom. 87

Approaching genetic complexity using forward and association

genetics
Charlotte Miller, Qingqing Xie, Han Wang, Ling Zhang, Eric Nguyen,
Jiahua Zhang, Qi Yu, Julian I. Schroeder, Wolfgang Busch.
Presenter affiliation: Salk Institute for Biological Studies, La Jolla,
California. 88

xviii
Abiotic stress response in shoot apical meristem—Identifying
gene regulatory networks that link shoot meristem development
and stress responses
Tie Liu.
Presenter affiliation: University of Florida, Gainesville, Florida. 89

Dead on time—Mechanisms controlling programmed cell death in

plant development
Rafael A. Buono, Norbert Bollier, Zongcheng Lin, Marta Cubria Radio,
Anna Daneve, Qiang-Nan Feng, Ellie Himschoot, Maria Simaskova,
Roman Hudecek, Marie L. Pfeiffer, Fei Xie, Klaas Vandepoele, Moritz
K. Nowack.
Presenter affiliation: VIB-UGent, Ghent, Belgium; Ghent University,
Ghent, Belgium. 90

New insights into maize ear development using single cell

(sc)RNA-Seq
Xiaosa Xu, Maggie Crow, Lei Liu, Carlos Ortiz-Ramírez, Liya Wang,
Doreen Ware, Kenneth Birnbaum, Jon Preall, Jesse Gillis, David
Jackson.
Presenter affiliation: Cold Spring Harbor Laboratory, Cold Spring
Harbor, New York. 91

The Arabidopsis TIR1/AFB auxin receptor genes have both

overlapping and specialized functions
Michael Prigge, Matthieu Platre, Wolfgang Busch, Mark Estelle.
Presenter affiliation: UCSD, La Jolla, California. 92

FRIDAY, December 6—5:00 PM

KEYNOTE SPEAKER

Introduction by: Zach Lippman, Cold Spring Harbor Laboratory

Cross-kingdom RNAi and small RNA trafficking between plants

and fungal pathogens
Qiang Cai, Baoye He, Shumei Wang, Hailing Jin.
Presenter affiliation: University of California, Riverside, Riverside,
California. 93

xix
 FRIDAY, December 6

BANQUET

Cocktails 6:00 PM Dinner 6:45 PM

SATURDAY, December 7—9:00 AM

SESSION 8 FRONTIER TECHNOLOGIES AND SYNTHETIC

BIOLOGY

Chairperson: Jim Haseloff, University of Cambridge, United Kingdom

Jim Haseloff.
Presenter affiliation: University of Cambridge, Cambridge, United
Kingdom.

A new long-read sequencing platform for genome assembly

Solomon Endlich, Ashby J. Morrison.
Presenter affiliation: Base5 Genomics, Inc, Menlo Park, California. 94

Engineering plant development to control root shape

Jennifer A. Brophy, Katie J. Magallon, Jose R. Dinneny.
Presenter affiliation: Stanford University, Stanford, California; Carnegie
Institution for Science, Stanford, California. 95

Unravel strigolactone signaling and controlling parasitic plant

behaviors with small molecules
Yuichiro Tsuchiya.
Presenter affiliation: Nagoya University, Nagoya, Japan. 96

The cis-regulatory landscape of maize single cells

Alexandre P. Marand, Zefu Lu, Xiaoyu Zhang, Robert J. Schmitz.
Presenter affiliation: University of Georgia, Athens, Georgia. 97

Breakthroughs in plant based PHB production—Harnessing

nature to heal nature
Kristi D. Snell, Meghna Malik, Oliver P. Peoples.
Presenter affiliation: Yield10 Bioscience, Woburn, Massachusetts. 98

xx
 AUTHOR INDEX

Abraham Juárez, María Jazmín, Brophy, Jennifer A., 95

28 Brueggeman, Robert S., 80
Abramson, Bradley W., 18 Buono, Rafael A., 90
Achom, Mingkee, 87 Burke, John, 5
Adhikari, Nirakar, 29 Burow, Gloria, 5
Agnew, Erica, 72 Busch, Wolfgang, 88, 92
Ahkami, Amir H., 19
Ahmed, Sheaza, 31 Cai, Qiang, 93
Alexandre, Cris, 9 Carneiro, Monalisa S., 26
Ali, Syed S., 46 Cartwright, Amy, 2
Alizadeh, Milad, 58 Castroverde, Christian D., 54
Allan, Andrew C., 55 Catalan, Pilar, 2
Ameen, Gazala, 80 Cates, Kitra L., 27
An, Hong, 84 Cavanagh, Amanda P., 81
Anderson, Justin, 13 Chalhoub, Boulos, 2
Angeles, Nathaniel, 38 Chen, Jin-Gui, 69
Anwar, Ammarah, 16 Chen, Junping, 5
Arikit, Siwaret, 20, 53 Chen, Zhong-Hua, 56
Ariyaratne, Menaka, 31 Chopra, Ratan, 5
Arkin, Adam, 37 Chougule, Kapeel, 24, 45, 60,
Arora, Deepika, 80 62, 64
Ayalew, Mentewab, 21 Christensen, Shawn, 5
Chu, Yi-Hsuan, 44
Balasubramanian, Vimal K., 19 Cleaves, Kailyn, 22
Baldwin, Robert, 50 Clough, Steven J., 65
Balekuttira, Somaiah T., 32 Cohen, Drew, 66
Banf, Michael, 73 Connolly, Erin L., 23
Barone, Lindsay C., 45 Contreras-Moreira, Bruno, 2, 60
Barrett, Jennifer, 72 Cooper, Elizabeth A., 23
Barry, Kerrie, 2 Cornet, Luc, 46
Bartlett, Madelaine E., 15, 28, 36 Cottingham, Bob, 37
Baxter, Ivan, 72 Coupland, George, 41
Baybayan, Primo, 62 Crow, Maggie, 91
Bennett, Morgan, 22 Cubria Radio, Marta, 90
Berendzen, Kenneth, 12 Cuperus, Josh T., 9, 30
Beveridge, Christine, 59 Czedik-Eysenberg, Angelika, 2
Birnbaum, Kenneth, 91 Czyz, Ewa, 17
Blumwald, Eduardo, 19
Bollier, Norbert, 90 Dampanaboina, Lavanya, 5
Börnke, Frederik, 83 Daneve, Anna, 90
Borowicz, Pawel P., 80 Dawe, Kelly, 24
Borrill, Philippa, 3 De Jaeger, Geert, 25
Bortlik, Jennifer, 83 De Leon, Natalia, 44
Brady, Siobhan, 70 De Winne, Nancy, 25
Brenton, Zachary W., 23 Demesa-Arevalo, Edgar, 36

xxi
D'Eustachio, Peter, 60 Guerinot, Mary Lou, 34, 49
Diaz-Perez, Antonio, 2 Gupta, Parul, 60
DiFazio, Stephen, 19
Dinh-Thi, Vinh Ha, 2 Han, Chao, 25
Diniz, Augusto L., 26 Haney, Cara H., 78
Dinneny, Jose R., 95 Hannigan, Brett, 24
Djamei, Armin, 2 Hartwick, Nolan, 18
Doonan, John, 2 Hasterok, Robert, 2
Dorrity, Michael, 9 Hayes, Chad, 5
Doseff, Andrea, 44 Hazen, Samuel, 2
He, Baoye, 93
Eeckhout, Dominique, 25 Heeney, Michelle, 36
Endlich, Solomon, 94 Henry, Christopher, 37
Eng, Kevin, 62 Herath, Venura, 29
Erb, Matthias, 84 Hermanson, Peter, 44
Espley, Richard V., 55 Hewezi, Tarek, 22
Estelle, Mark, 92 Himschoot, Ellie, 90
Ethridge, Christina L., 27 Hirsch, Candice, 24, 44
Hirsch-Hoffmann, Matthias, 46
Farmer, Andrew, 39 Holland, Cynthia K., 84
Feiz, Leila, 77 Hsu, Fei-Man, 45
Feng, Qiang-Nan, 90 Hu, Fangle, 70
Fengler, Kevin, 24 Huang, Shao-shan Carol, 38
Fernandez-Marco, Cristina, 47 Hubbard, Allen, 72
Fields, Stanley, 30 Hudecek, Roman, 90
Freudenthal, Jan, 16 Hudson, Matthew, 65
Fritschi, Katrin, 12 Hufford, Matthew, 24
Fungtammasan, Chai, 24 Humphreys, Jazmine, 59

Gadeyne, Astrid, 25 Jackson, David, 36, 91

Gallagher, Joseph P., 15, 28 Jaiswal, Pankaj, 60
Gaudinier, Allison, 70 Jander, Georg, 77, 84
Gayral, Mathieu, 29 Jegadeeson, Vidya, 56
Gehring, Mary, 7, 52, 66 Jenkins, Jerry, 2
Gerber, Scott A., 34 Ji, Lexiang, 11, 71
Ghahrehmani, Mina, 46 Jiang, Hui, 72
Ghiban, Cornel, 45 Jiao, Yinping, 5, 24, 60, 62, 64
Gifford, Miriam L., 87 Jin, Hailing, 93
Gillis, Jesse, 91 Johnson-Cicalese, Jennifer, 33
Gladman, Nicholas, 5 Jores, Tobias, 30
Goltsman, Eugene, 2 Joshi, Kumud, 31
Goméz, José María, 84 Juarez, Maria, 36
Gomez, Lina, 44 Julian, Russell S., 32
Gonzalez, Julia Q., 13
Goodstein, David, 2 Kaczmarek, Joanna, 79
Gordon, Sean, 2 Kalinoski, Andrea, 31
Gray, John, 44 Karey Tello-Ruiz, Marcela, 47
Grotewold, Erich, 44 Katz, Andrew, 2

xxii
Kaur, Ravneet, 39 Lutz, Ulrich, 43
Kawash, Joseph K., 33
Ke, Lanlan, 67 Mabry, Mackenzie E., 84
Kemi, Ulla, 41 Magallon, Katie J., 95
Kerr, Stephanie, 59 Magnusson, Erika, 44
Khangura, Rajdeep S., 45 Mahmoud, Soheil, 50
Kim, Sun A, 34 Maiochi, Iago, 26
Kjellbom, Per O., 35 Malik, Meghna, 98
Klein, Harry, 28, 36 Man, Jarrett A., 15
Korte, Arthur, 16 Marand, Alexandre P., 11, 97
Kraemer, Ute, 13 Marco, Cristina F., 45
Krasileva, Ksenia V., 8 Markillie, Lye Meng, 19
Kresovich, Stephen, 23 Martin, Joel, 2
Kuchuk, Mykola, 57 Matthijs, Caroline, 25
Kumar, Pavan, 84 May, Jared P., 4
Kumar, Vivek, 37, 60 Mehta, Devang, 46
Kumari, Sunita, 37, 60 Meijs, Ivar, 64
Kumbale, Carla, 21 Meja, Sendi, 47
Kurosky, Alexander, 54 Mendieta, John P., 48
Mercier, Raphael, 10
Lacombe, Benoit, 14 Merry, Ryan, 61
LaCroix, Ian S., 34 Michael, Todd, 18
Lagunas, Beatriz, 87 Micklos, David A., 45
Lasky, Jesse, 6 Miller, Charlotte, 88
Lee, Gwonjin, 13 Miller, Rita, 29
Lee, Scott, 2 Mirzaei, Mahdieh, 84
Lee, Young Koung, 5 Mockler, Todd, 72
Levy, Joshua, 2 Monroe, Grey, 12
Li, Cheng, 17 Morris, Paul F., 31
Li, Miaomiao, 38 Morrison, Ashby J., 94
Li, Xiaoping, 72 Morsdorf, Felix, 17
Li, Ying, 32 Movahed, Navid, 77
Liang, Ping, 50 Mu, Shuai, 49
Libault, Marc, 39 Muchero, Wellington, 69
Lin, Chen-Yu, 40 Muehlbauer, Gary J., 61
Lin, Yao-Cheng, 40 Mueller, Lukas A., 84
Lin, Yi-Chen, 41 Müller, Caroline, 84
Lin, Zongcheng, 90 Muna, Demitri, 45
Liu, Jianing, 24 Mur, Luis, 2
Liu, Lei, 91 Murphy, Nathalie G., 27
Liu, Tie, 89 Mwaura, Bethany, 21
Liya, Liya, 45
Llaca, Victor, 24 Naithani, Sushma, 60
Lopez, William, 16 Nattamai Malli
Lorenz, Aaron J., 61 Pooranachandhiran, Radesh,
Lu, Zefu, 11, 27, 97 50
Lu, Zhenyuan, 42, 63 Nazar, Ross N., 54
Lusinska, Joanna, 2 Nguyen, Cuong X., 51

xxiii
Nguyen, Eric, 88 Rodrigues, Jessica A., 55
Nibau, Candida, 2 Rodriguez, Maria, 46
Noutsos, Christos, 47 Rokhsar, Daniel, 2
Nowack, Moritz K., 90 Rono, Catherine, 21
Roy, Proyash, 87
Olson, Andrew, 45, 60, 62, 64, Rubio Wilhelmi, Maria D., 19
70 RV, Satyaki P., 52
Olsson, Olof, 68
Ort, Donald R., 81 Sajeevan, Radha S., 56
Ortiz-Ramírez, Carlos, 91 Sancho, Ruben, 2
Ou, Jheng-Yang, 40 Santos, Lucas B., 65
Sapkota, Sirjan, 45
Paddock, Kyle J., 51 Sattely, Elizabeth, 82
Papatheodorou, Irene, 60 Sawikowska, Aneta, 79
Parthasarathy, Pavithra, 56 Schaepman, Michael E., 17
Peoples, Oliver P., 98 Schäfer, Patrick, 87
Pérez-Fernández, María, 46 Schläpfer, Pascal, 72, 73
Perfectti, Francisco, 84 Schmid, Bernhard, 17
Persiau, Geert, 25 Schmitz, Robert J., 11, 27, 48,
Petschenka, Georg, 84 71, 97
Pfeiffer, Marie L., 90 Schmutz, Jeremy, 2, 69
Piasecka, Anna, 79 Schroeder, Julian I., 88
Pietzenuk, Bjoern, 13 Schuman, Meredith C., 17
Pires, Chris, 84 Schwechheimer, Claus, 43
Platre, Matthieu, 92 Seaver, Sam, 37
Plaxton, William C., 46 Seetharam, Arun, 24
Plott, Chris, 2 Sellamuthu, Gothandapani, 56
Polashock, James J., 33 Sergaki, Chrysa, 87
Powell, Adrian F., 84 Session, Adam, 2
Preall, Jon, 91 Shabala, Lana, 56
Preece, Justin, 60 Shabala, Sergey, 56
Prigge, Michael, 92 Shih, Patrick M., 85
Purvine, Samuel, 19 Shimizu, Kentaro K., 17
Shittu, Hakeem O., 54
Qiao, Pengfei, 45 Shu, Shenquaing, 2
Qu, Shujun, 24 Siangliw, Meechai, 53
Queitsch, Christine, 9, 30 Simaskova, Maria, 90
Simon, Anne E., 4
Radutoiu, Simona, 76 Sindarovska, Yana, 57
Rajakani, Raja, 56 Singan, Vasanth, 2
Ramírez-González, Ricardo, 3 Sjaarda, Calvin, 50
Ray, Christopher, 59 Snell, Kristi D., 98
Regulski, Michael, 5, 62 Solanki, Shyam, 80
Rhee, Sue, 72, 73 Song, Liang, 58
Riangwong, Kanamon, 53 Song, Yuanyuan, 67
Ricci, William A., 11, 48 South, Paul F., 81
Richmond, Bethany L., 87 Souza, Anete P., 65
Robb, Jane, 54 Souza, Glaucia M., 26

xxiv
Sowdhamini, R, 56 Wang, Jin, 86
Spencer, Madison, 61 Wang, Liya, 42, 62, 63, 91
Springer, Nathan, 44 Wang, Shumei, 93
Srikant, Thanvi, 12 Wang, Xiaofei, 63
Stacey, Minviluz G., 51 Wang, Yangzi, 67
Städler, Thomas, 67 Wang, Zhi-Yong, 74
Stec, Adrian O., 61 Ware, Doreen, 5, 24, 26, 37, 42,
Stein, Joshua, 64 45, 47, 60, 62, 63, 64, 70, 91
Stewart, Neal, 19 Wasikowski, Rachael, 45
Stickler, Susan R., 84 Waskiewicz, Agnieszka, 79
Stitzer, Michelle C., 45 Wei, Sharon, 60, 64
Stupar, Robert M., 61 Wei, Wei, 65
Weigel, Detlef, 1, 12, 43
Tanurdzic, Milos, 59 Weix, Sharon, 24
Tartaglio, Virginia, 2 Wendte, Jered M., 71
Tello-Ruiz, Marcela K., 45, 60, Whipple, Clinton, 36
64 Wibowo, Anjar, 12
Thibivilliers, Sandra, 39 Williams, Ben P., 66
Toojinda, Theerayut, 53 Witaszak, Natalia, 79
Tseng, Elizabeth, 62 Wolfrum, Edward J., 72
Tsuchiya, Yuichiro, 96 Wolny, Elzbieta, 2
Tuskan, Gerald, 69 Wu, Hao, 45
Wu, Xing, 65
Uauy, Cristobal, 3
Uhrig, R. Glen, 46 Xie, Fei, 90
Unartngam, Jintana, 53 Xie, Qingqing, 88
Xin, Zhanguo, 5
Van Buren, Peter, 42, 62 Xu, Shuqing, 67
Van De Slijke, Eveline, 25 Xu, Xiaosa, 36, 91
Van Leene, Jelle, 25 Xu, Xin, 54
Vanavichit, Apichart, 20
Vandepoele, Klaas, 90 Yong, Yongil, 19
Vanderschuren, Hervé, 46 York, Thomas, 84
Varala, Kranthi, 32 Yu, Qi, 88
Vasylenko, Maksym, 57 Yuan, Wei, 12
Venkataraman, Gayatri, 56
Verchot, Jeanmarie, 29 Zambrano, Jose A., 68
Viana, Joao P., 65 Zeng, Renseng, 67
Vimalarani, Shoban K., 32 Zhan, Junpeng, 45
Virdi, Kamaldeep S., 61 Zhang, Jiahua, 88
Vogel, John, 2 Zhang, Jin, 69
Voit, Eberhard, 21 Zhang, Lifang, 5, 70
Vorsa, Nicholi, 33 Zhang, Ling, 88
Zhang, Xiaoyu, 11, 97
Walker, Liam, 87 Zhang, Yinwen, 71
Wanchana, Samart, 20, 53 Zhang, Zhanyuan, 51
Wang, Bo, 24, 60, 62, 64 Zhao, Cheng, 72
Wang, Han, 88 Zhao, Kangmei, 73

xxv
Zheng, Luqing, 49
Zheng, Po-Xing, 40
Zhou, Jian-Min, 75
Zhou, Meixue, 56
Zhou, Peng, 44
Zhu, Jia-Ying, 74
Zhu, Ying, 19
Züst, Tobias, 84

xxvi
EPISTASIS, THE SPICE OF LIFE: LESSONS FROM THE STUDY OF
THE PLANT IMMUNE SYSTEM

Detlef Weigel

Max Planck Institute for Developmental Biology, Dept. of Molecular

Biology, Tübingen, Germany

My group is addressing fundamental questions in evolutionary biology,

using both genome-first and phenotype-first approaches. A few years ago,
we discovered that Arabidopsis thaliana is a great model for the study of
hybrid necrosis. This widespread syndrome of hybrid failure in plants is
caused by plant paranoia – regardless of the presence of enemies, plants
“think” they are being attacked by pathogens. The consequence is
autoimmunity, which can be extreme enough to kill plants before they set
seeds.
Over the past decade, we have studied in detail the underlying genetics,
finding that often only one or two loci are involved, with most of them
encoding NLR immune receptors. The NLR gene family is the most
variable gene family in plants, and it is thus not surprising that they are
often involved in genome-genome conflict. Similarly, we have found that
autoimmunity due to allelic variation at the ACD6 locus, which probably
encodes a channel, is modulated by a slew of extragenic suppressors. I will
describe what we have learned and how our unique angle on studying the
plant immune system has led to insights that were not obtained with
conventional laboratory genetics.
Our goal for the next decade is to understand the genomic and geographic
patterns of immune system diversity. Together with collaborators Jeff
Dangl, Jonathan Jones and Brian Staskawicz, we have been describing
species-wide diversity of NLR immune receptor genes. In parallel, we have
been describing with collaborator Eric Kemen the local diversity of the
microbial pathogen, Pseudomonas, on A. thaliana plants. This year, we
initiated an ambitious new project, Pathodopsis (Patho[gens in
Arabi]dopsis), in which we aim to describe genetic diversity in the host and
two important pathogens, the generalist Pseudomonas and the specialist
Hyaloperonospora arabidopsidis. The long-term vision is to produce maps
of resistance alleles in the host, and of effector alleles in the pathogens, in
order to learn who normally wins in a wild plant pathosystem – the host or
the pathogen.

Additional information about our work can be found on our websites,

http://weigelworld.org and http://pathodopsis.org.

1
GRADUAL POLYPLOID GENOME EVOLUTION REVEALED BY A
PAN-GENOMIC ANALYSIS OF BRACHYPODIUM HYBRIDUM AND
ITS DIPLOID PROGENITORS

Sean Gordon1, Bruno Contreras-Moreira2, Joshua Levy1,3, Armin Djamei4,

Angelika Czedik-Eysenberg4, Virginia Tartaglio1,3, Adam Session1, Joel
Martin1, Amy Cartwright1, Andrew Katz1, Vasanth Singan1, Eugene
Goltsman1, Kerrie Barry1, Vinh Ha Dinh-Thi5, Boulos Chalhoub5, Antonio
Diaz-Perez6, Ruben Sancho6, Joanna Lusinska7, Elzbieta Wolny7, Candida
Nibau8, John Doonan8, Luis Mur8, Chris Plott9, Jerry Jenkins9, Samuel
Hazen10, Scott Lee10, Shenquaing Shu1, David Goodstein1, Daniel
Rokhsar1,3, Jeremy Schmutz1,9, Robert Hasterok7, Pilar Catalan6, John
Vogel1,3
1
DOE Joint Genome Institute, Walnut Creek, CA, 2Estación Experimental
de Aula Dei, Zaragoza, Spain, 3University of California, Berkeley,
Berkeley, CA, 4Gregor Mendel Institute of Molecular Plant Biology,
Vienna, Austria, 5Institut National de la Recherche Agronomique,
Versailles, France, 6Universidad de Zaragoza-Escuela Politécnica Superior
de Huesca, Huesca, Spain, 7University of Silesia in Katowice, Department
of Plant Anatomy and Cytology, Katowice, Poland, 8Aberystwyth
University, Aberystwyth, Wales, United Kingdom, 9Hudson Alpha Institute
for Biotechnology, Huntsville, AL, 10University of Massachusetts Amherst,
Biology Department, Amherst, MA

Our understanding of polyploid genome evolution is constrained because

we cannot know the exact founders of natural polyploid species. To
differentiate between founder effects and post-polyploidization evolution,
we used a pan-genomic approach to study the allotetraploid Brachypodium
hybridum and its extant diploid progenitors B. distachyon and B. stacei.
Comparative analysis revealed that the vast majority of B. hybridum whole
gene presence/absence variation (PAV) overlapped with B. distachyon
PAV. Analysis of nuclear single nucleotide variants (SNVs), plastomes and
k-mers revealed two independent origins for B. hybridum, ~1.4 and ~0.14
million years ago. We noted small but significant accumulation of
polyploid-specific SNVs and small indels in the younger B. hybridum
lineage and a much larger number of polymorphisms in the older B.
hybridum lineage. These results are consistent with gradual genomic
changes after polyploidization. In addition, our data indicate that the two
observed B. hybridum clades remain genetically distinct, despite being
geographically overlapping. This suggests an ongoing barrier to genetic
exchange, which we experimentally confirmed via controlled crosses. This
highlights the fact that allopolyploid species may be composed of different
clades formed at different times from divergent diploid progenitors of the
same species. Significantly, if we did not use a pan-genomic approach we
would have grossly overestimated the number of genomic changes
attributable to post polyploidization evolution.

2
TOWARDS MECHANISTIC UNDERSTANDING OF HOMOEOLOG
EXPRESSION LEVELS IN POLYPLOID WHEAT

Philippa Borrill1, Ricardo Ramírez-González2, Cristobal Uauy2

1
University of Birmingham, School of Biosciences, Birmingham, United
Kingdom, 2John Innes Centre, Crop Genetics, Norwich, United Kingdom

Polyploidy is common within many plant species. The highly related gene
copies, known as homoeologs, found in polyploids are proposed to confer
adaptive advantages for example through tissue-specific expression of
duplicated genes or neofunctionalisation. However little is known about
how gene expression is regulated within these complex genomes. We are
using wheat, with its sequenced genome, extensive RNA-seq datasets and
long history of genetic studies to explore how homoeolog expression is
regulated.

We investigated homoeolog-specific gene expression in wheat using an

extensive set of 850 RNA-seq samples from diverse tissues, cultivars and
developmental stages. On average 30 % of triads (a set of three
homoeologs) showed nonbalanced expression patterns, with over- or under-
expression of one homoeolog compared to the other two. We identified that
differences in homoeolog expression were associated with epigenetic
changes in histone modifications and DNA methylation. We found that
homoeologs changed their expression levels between different tissues, and
these transcriptionally dynamic homoeologs are under more relaxed
selection pressure, which may represent the first steps towards functional
diversification.

Several major agronomic traits are controlled by changes in the expression

level of one homoeolog between cultivars including VRN1 and PPD1 that
have been essential to adapt wheat flowering to a range of environmental
conditions. These well-studied genes are not unique in showing differences
in the expression levels of homoeologs between cultivars and our current
work suggests that these differences in homoeolog expression can be
inherited. Furthermore the expression level of homoeologs within a triad are
frequently rebalanced in offspring compared to the parents. We are
investigating the mechanisms which control the inheritance of homoeolog
expression levels. This work may ultimately lead to routes to manipulate
homoeolog expression for crop improvement.

3
RNA VIRUS EVASION OF NONSENSE MEDIATED DECAY

Anne E Simon, Jared P May

University of Maryland, Dept. of Cell Biology and Molecular Genetics,

College Park, MD

Nonsense-mediated decay (NMD) serves a critical role in preserving the

integrity of the host transcriptome. RNA transcripts bearing premature
termination codons (PTCs) are subject to NMD as they can lead to
expression of truncated, deleterious proteins, which are associated with
many genetic diseases and cancer. While it is known that long 3’ UTRs
promote NMD, many mRNAs with long 3’ UTRs are protected, but the
mechanism(s) involved in this protection were not understood. Natural stop
codons in the genomes of multicistronic RNA plant viruses resemble PTCs
and thus these viruses must have developed mechanisms to combat NMD to
maintain genome stability. We investigated how two single component,
positive sense RNA virus evade NMD. Turnip crinkle virus evades NMD
by several mechanisms: (1) the presence of a translational readthrough
element that is responsible for synthesis of the viral RNA-dependent RNA
polymerase; and (2) an unstructured region following the coat protein ORF.
We have found that sequence-non-specific, unstructured regions of RNA
following stop codons can confer NMD-resistance to normally sensitive
transcripts and this trend was also observed in a set of previously described
NMD-resistant human transcripts. In contrast, umbravirus Pea enation
mosaic virus 2 (PEMV2) uses long-distance movement protein p26 to
overcome NMD. p26 was previously shown to both stabilize viral RNAs
and bind them for transport through the plant’s vascular system. p26
protects both viral and non-viral messenger RNAs from NMD, which likely
involves its RNA binding activity and ability to form large inclusion bodies.
Using a transcriptome-wide approach in the model plant Nicotiana
benthamiana, p26 protected a subset of cellular NMD-target transcripts,
particularly those containing long, structured, GC-rich 3’ UTRs.
Furthermore, RNA-seq revealed that the NMD pathway is highly
dysfunctional during PEMV2 infection, with 1,820 (48%) NMD-targets
increasing in abundance. Widespread changes in the host transcriptome is
common during plant RNA virus infections and our findings suggest that
virus-mediated NMD-inhibition may be a major contributing factor.

4
FERTILITY OF PEDICELLATE SPIKELETS IN SORGHUM IS
CONTROLLED BY A JASMONIC ACID REGULATORY MODULE

Nicholas Gladman1,2, Yinping Jiao1,2, Young Koung Lee2,3, Lifang Zhang2,

Ratan Chopra4, Michael Regulski2, Gloria Burow1, Chad Hayes1, Shawn
Christensen5, Lavanya Dampanaboina1, Junping Chen1, John Burke1,
Doreen Ware2,6, Zhanguo Xin1
1
Agricultural Research Service, Plant Stress and Germplasm Development
Unit, Cropping Systems Research Laboratory, Lubbock, TX, 2Cold Spring
Harbor Laboratory, Ware Lab, Cold Spring Harbor, NY, 3National Fusion
Research Institute, Plasma Technology Research Center, Dongjangsan-ro,
South Korea, 4University of Minnesota, Department of Agronomy and Plant
Genetics, St. Paul, MN, 5Agricultural Research Service, Chemistry
Research Unit, Gainesville, FL, 6Agricultural Research Service, NEA
Robert W. Holley Center for Agriculture and Health, Ithaca, NY

As in other cereal crops, the panicles of sorghum (Sorghum bicolor (L.)

Moench) comprise two types of floral spikelets (grass flowers). Only sessile
spikelets (SSs) are capable of producing viable grains, whereas pedicellate
spikelets (PSs) cease development after initiation and eventually abort.
Consequently, grain number per panicle (GNP) is lower than the total
number of flowers produced per panicle. The mechanism underlying this
differential fertility is not well understood. To investigate this issue, we
isolated a series of EMS-induced multiseeded (msd) mutants that result in
full spikelet fertility, effectively doubling GNP. Previously, we showed that
MSD1 is a TCP (Teosinte branched/Cycloidea/PCF) transcription factor
that regulates jasmonic acid (JA) biosynthesis, and ultimately floral sex
organ development. Here, we show that MSD2 encodes a lipoxygenase
(LOX) that catalyzes the first committed step of JA biosynthesis. Further,
we demonstrate that MSD1 binds to the promoters of MSD2 and other JA
pathway genes. Together, these results show that a JA-induced module
regulates sorghum panicle development and spikelet fertility. The findings
advance our understanding of inflorescence development and could lead to
new strategies for increasing GNP and grain yield in sorghum and other
cereal crops.

5
GENOMICS OF SORGHUM LOCAL ADAPTATION TO A PARASITIC
PLANT

Jesse Lasky

Pennsylvania State University, Department of Biology, University Park, PA

Host-parasite coevolution can maintain high levels of genetic diversity in

traits involved in species interactions. In many systems, host traits exploited
by parasites are constrained by use in other functions, leading to complex
selective pressures across space and time. Here, we study genome-wide
variation in the staple crop Sorghum bicolor and its association with the
parasitic weed Striga hermonthica, a major constraint to food security in
many African countries. We hypothesize that sorghum landraces are subject
to geographic selection mosaics within parasite-prone areas and selection
against resistance where S. hermonthica is never found. Supporting this
hypothesis, multiple independent loss-of-function alleles at sorghum LOW
GERMINATION STIMULANT 1 (LGS1), a locus known to impact
resistance, are broadly distributed among African landraces and
geographically associated with S. hermonthica occurrence, suggesting a role
in local adaptation to parasite pressure. However, the low frequency of
these alleles within S. hermonthica-prone regions and their absence
elsewhere indicates potential trade-offs restricting their distribution. LGS1
impacts stereochemistry of strigolactones, hormones controlling plant
architecture, belowground signaling with other organisms, and abiotic stress
tolerance. To test for trade-offs, we created CRISPR LGS1 deletions and
found that their resistance to Striga parasites was reduced for certain
populations of the parasite Striga. We also found that the deletions
exhibited broad transcriptome differences in downstream strigolactone
signalling, suggesting potentially costly pleiotropy. Signatures of balancing
selection surrounding LGS1 and candidates from analysis of genome-wide
associations with parasite distribution support long-term maintenance of
diversity in parasite resistance genes. Our study of host resistance evolution
across smallholder agroecosystems provides a valuable contrast to both
industrial farming systems and natural communities.

6
EPIGENETIC PROCESSES AT THE SINGLE CELL LEVEL:
ANALYSIS OF ARABIDOPSIS IMPRINTING DYNAMICS

Mary Gehring

Whitehead Institute, MIT, Cambridge, MA

Imprinting serves as an excellent case study for deciphering epigenetic

mechanisms of gene regulation. Alleles of imprinted genes are differentially
expressed in a parent-of-origin dependent manner. In plants, gene
imprinting occurs in a triploid seed tissue, the endosperm. Differential DNA
methylation and PRC2-directed modifications are important for establishing
and maintaining imprinted expression. Previous genomic studies have
identified all Arabidopsis imprinted genes and defined the relationship
between imprinting and epigenetic modifications. These studies show that
many instances of imprinting are partial, meaning genes are biased toward
expression from one allele, but expression is not completely monoallelic.
There are two possible interpretations for this result: 1) both alleles are
transcribed in an individual cell but at different levels or 2) there is cell-to-
cell variation in whether or not a gene is imprinted. We are addressing these
questions by performing allele-specific gene expression profiling in
individual endosperm nuclei. In addition to defining new cell states within
endosperm tissue, we have found that paternally expressed imprinted genes
are more variably imprinted than maternally expressed imprinted genes.
These results have important implications for understanding imprinting
mechanisms and the potential relationship to DNA methylation.

7
NATURAL DIVERSITY IN HIGHLY VARIABLE PLANT NLR
IMMUNE RECEPTORS

Ksenia V Krasileva

University of California, Berkeley, Plant and Microbial Biology, Berkeley,

CA

Plant immunity depends either on direct perception of pathogen molecules

or of the changes they induce in the host cells. Both recognition modes
require mechanisms for generating diversity in the plant immune receptors.
We have previously demonstrated that grasses deploy a specialist
intracellular NLR immune receptor clade that undergoes continuous gene
fusions incorporating protein domains not normally associated with the
immune function. The newly integrated domains in these NLR-ID receptors
serve as baits for the pathogen - their modification triggers immune
signalling. Such deployment of other plant proteins as baits allows plant
immunity to monitor changes that pathogens induce inside the host cell. Our
current work addresses the sources of new receptor specificities in the direct
recognition of pathogen derived effectors. We show that a quarter of NLR
immune receptors in the model plant A. thaliana evolve much faster than
the rest with changes concentrated in the leucine-rich repeat domain. These
genes show a strong overlap with the hybrid incompatibility loci, suggesting
that generation of new immune specificities comes at a cost of
autoimmunity. While separated in sequence, the most variable residues
cluster on the concave surface of the LRR, allowing prediction of putative
effector-binding sites. Together, our analyses uncover distinct mechanisms
of diversity generation among different groups of plant NLR receptors.

8
IDENTIFYING CHROMATIN-ACCESSIBLE REGIONS THAT
ACTIVELY DRIVE GENE EXPRESSION

Michael Dorrity, Cris Alexandre, Christine Queitsch, Josh T Cuperus

University of Washington, Genome Sciences, Seattle, WA

Cis-regulatory regions are critical to domestication and trait improvement,

however few distal regions known to influence gene expression are known.
Furthermore, the chromatin accessibility landscape is quiet static across
plant tissues or conditions, with at most 5-10% changing. This lack of
dynamic accessibility is likely due to both tissue heterogeneity and poised
transcription factors that do not move. To assess both of these possibilities
we have used single-cell genomics, both RNA-seq and ATAC-seq, to get to
cell-type specific accessibility; and massively parallel reporter assays to
assay which accessible regions are truly driving gene expression. Using
both will guide us in understanding which changing accessible regions are
truly driving gene expression in crops, with the overall mission to be able to
drive expression in a cell-type specific manner to alter crops for trait
improvement and increased yields without having large pleiotropic effects
on phenotypes and gene expression. Currently, we have single-cell ATAC-
seq on several Arabidopsis tissues, and can identify several distinct cell
types including all major cell types of the root, as well as major floral
organs at early and mature developmental stages. scATAC analysis of early
and mature flowers revealed several distinct developmental trajectories and
identified stage-specific cell clusters that correspond to the developing
anther and carpel. Using new technologies for alignment of single-cell
datasets generated for different molecular phenotypes (both RNA and
ATAC, for example), we provide further definition of cell identities in the
Arabidopsis root. We will use these data to better understand the link
between gene regulatory events and the transcriptional programs that define
cell identity in plant tissues.

9
WHAT LIMITS MEIOTIC RECOMBINATION?

Raphael Mercier1,2
1
Max Planck Institute for Plant Breeding Research, Chromosome Biology,
Cologne, Germany, 2INRA, Jean-Pierre Bourgin Institute, Versailles,
France

Meiotic crossovers shuffle parental genetic information, providing novel

combinations of alleles on which natural or artificial selection can act.
However, meiotic crossovers are relatively rare, typically one to three per
chromosome, limiting the efficiency of the breeding process and related
activities such as genetic mapping. This also raises the question of the
evolutionary forces that maintain this low level of crossovers.

Using a forward genetic screen, we identified a series of genes that limit

meiotic recombination in Arabidopsis, defining three anti-crossover
pathways relying on different molecular activities. We analysed meiotic
recombination in Arabidopsis plants in which one, two, or all three of these
pathways were disrupted. The greatest effect was observed when combining
recq4 and figl1 mutations, which increased the hybrid genetic map length
more than 7 folds. Our findings show that, although most eukaryotes have
only one to three crossovers per chromosome on average, crossover number
can be largely increased without obvious negative phenotypic effects,
suggesting that crossovers are naturally constrained below their possible
maximum.

We then explored the effects of mutating these pathways on recombination

in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and
tomato (Solanum lycopersium). We found that the single recq4 mutation
increases crossovers ~three-fold in these crops, suggesting that
manipulating RECQ4 may be a universal tool for increasing recombination
in plants.
We are now exploring the potential of enhanced recombination for plant
breeding research.

10
WIDESPREAD LONG-RANGE CIS-REGULATORY ELEMENTS IN
THE MAIZE GENOME

William A Ricci1, Zefu Lu2, Lexiang Ji2, Alex P Marand2, Robert J

Schmitz2, Xiaoyu Zhang1
1
University of Georgia, Plant Biology, Athens, GA, 2University of Georgia,
Genetics, Athens, GA

Genetic mapping studies on crops suggest that agronomic traits can be

controlled by loci from within the gene-distal intergenic space. Despite the
biological importance and the potential agronomic utility of these intergenic
loci, they remain virtually uncharacterized in all crop species to date. Here,
we provide genetic, epigenomic, and functional molecular evidence
supporting the widespread existence of gene-distal loci which act as long-
range transcriptional cis-regulatory elements (CREs) in the maize genome.
Such loci are enriched for euchromatic features that suggest their regulatory
functions. Chromatin loops link together putative CREs with genes and
recapitulate genetic interactions. Additionally, putative CREs display
elevated transcriptional enhancer activities, as measured by STARR-seq.
These results provide functional support for the widespread existence of
CREs which act over large genomic distances to control gene expression.

11
THE A. THALIANA METHYLOME INFLUENCES CHROMATIN
ACCESSIBILITY AFTER HEAT STRESS

Thanvi Srikant1, Wei Yuan1, Anjar Wibowo1,2, Kenneth Berendzen3, Katrin

Fritschi1, Grey Monroe1, Detlef Weigel1
1
Max Planck Institute for Developmental Biology, Department of Molecular
Biology, Tuebingen, Germany, 2Airlangga University, Faculty of Science
and Technology, Surabaya City, Indonesia, 3University of Tuebingen,
ZMBP Central Facilities, Tuebingen, Germany

Plants face a multitude of stresses during their lifetime, and in response alter
their chromatin architecture to facilitate changes in gene expression.
Previous studies of the chromatin landscape in the model plant Arabidopsis
thaliana have identified novel sites in the genome that function as
regulatory elements upon increased access to transcription machinery (Lu et
al. 2017). We are interested in understanding how cytosine DNA
methylation, a prominent epigenetic mark in A. thaliana, regulates gene
expression via its effect on chromatin conformation.

We used Assay for Transposase-Accessible Chromatin followed by

sequencing (ATAC-seq, Buenrostro et al. 2015) to investigate genome-wide
differences in chromatin accessibility between A. thaliana lines
differentiated by global epigenetic states: Col-0 wild type and met1-1, a
knockout mutant that exhibits genome-wide CG hypomethylation in the
same background (Kankel et al. 2003). We subjected both genotypes to an
acute heat stress (90 minutes at 45 °C), to probe effects on chromatin
structure. We find that heat induction perturbs chromatin integrity, with 146
regions statistically significant for genotype-independent differences arising
from stress-treatment, 139 regions for genotype-specific effects, and 128
regions for genotype-by-treatment effects. These indicate that acute heat
stress perturbs chromatin structure, and its effect is dependent on the
methylome of the plant.

We are integrating methylome, transcriptome, genome-wide polymorphism

information with our ATAC-seq dataset, to examine the roles of
differentially accessible loci in temporal transcriptional regulation, and its
potential effect in structural evolution of the genome. Taken together, we
aim to achieve a better understanding of the mechanisms underlying
genome stability under stress, driven by epigenetic interactions.

12
ADAPTATION TO LOCAL SOIL COMPOSITION IN ARABIDOPSIS
HALLERI

Gwonjin Lee1, Julia Q Gonzalez1, Justin Anderson1,2, Bjoern Pietzenuk1,

Ute Kraemer1
1
Ruhr University Bochum, Molecular Genetics and Physiology of Plants,
Bochum, Germany, 2Nunhems (BASF Vegetable Seeds), Nunhem,
Netherlands

Plants require merely inorganic nutrients and form the basis of diverse
ecosystems around the globe as central mediators between the inorganic and
the living world. To survive, plants must accomplish nutritional balancing
because soil mineral composition always deviates from internal nutritional
needs. Moreover, soil composition varies vastly in both space and time, so
that all plants are capable of acclimation, and well-known soil type-specific
plant communities constitute vivid examples of local adaptation. Our
objective is to understand the molecular bases, ecological functions and
evolution of plant adaptations to soil composition in Arabidopsis halleri.
This outcrossing diploid stoloniferous perennial is a suitable model
organism because of the extreme nature and large within-species diversity
of its interactions with soil, in combination with a phylogenetic position
among the sister species of the genetic model plant A. thaliana. In order to
address within-species diversity, we established a collection of ca. 850
living A. halleri individuals from 165 populations across Europe, for which
we documented mineral composition of leaves and of individual soil micro-
environments together with other environmental parameters at the site of
origin in the fielda, accompanied by genotyping-by-sequencing-based
genome-wide genetic information. A. halleri is common at metalliferous
sites highly contaminated with the heavy metals zinc, cadmium, copper and
lead, but the majority of its populations exist on pristine uncontaminated
soils. Species-wide hyperaccumulation of Zn (>3,000 µg g-1 dry leaf
biomass) and the phylogeographically confined hyperaccumulation of Cd
(>100 µg g-1) in A. halleri occur on both metalliferous and non-
metalliferous soils. We consider hyperaccumulation an analytically
accessible trait exemplifying the co-option of minerals, i.e. their use in
functions unrelated to the maintenance of metabolic, structural and
developmental functions, for example the defence against biotic stress.
Based on genome-wide sequence data, we combine marker association,
genome scan, genetic linkage mapping, and transcriptomic approaches with
the targeted analysis of molecular functions. The status of results will be
presented focusing on parallel evolutionb and plant adaptation to heavy
metal pollution as an example of a rapid extreme anthropogenic
environmental change.
a
Stein et al. (2017) doi:10.1111/nph.14219; bPreite et al. (2019)
doi:10.1098/rstb.2018.0243

13
PROTEIN AND GENE REGULATORY NETWORK INVOLVED IN
HORMONE-DEPENDENT NUTRIENT SENSING

Benoit Lacombe

CNRS, Biochimie et Physiologie Moléculaire des Plantes, Montpellier,

France

To optimize their growth and development plants are able to sense their
environment and to modulate their development. Beside its role as nitrogen
(N) source, nitrate (NO3-) is a signaling molecule involved in different
physiological responses. The effect of nitrate on lateral root development
has been described with a local and a systemic component.
We used a combination of functional screen in heterologous expression
systems (Xenopus oocytes, COS cells, Yeast), transcriptomics, hormone
quantification and root development analysis to identify the gene and
protein regulatory networks involved in this nitrate-dependent signaling.
We have identified NPF transporters that are part of protein regulatory
network built with transporters/CIPK/CBL and PP2C involved in hormone
dependent nutrient sensing in Arabidopsis. This demonstrates a link
between ABA and nutrient transport and sensing. These crosstalks are
further supported by the identification of ABA transporters in the NPF
family also regulated CIPK/CBL/PP2C.
Other approaches initiated to identify the molecular bases of nitrate-
hormone crosstalks will be presented.

14
STRUCTURAL VARIATION IN THE LRR-RLK GENE FAMILY
DRIVES RECEPTOR DIVERSIFICATION

Jarrett A Man, Joseph P Gallagher, Madelaine E Bartlett

University of Massachusetts Amherst, Biology, Amherst, MA

Developmental and defense processes are cued by complex mixtures of

extracellular chemical signals. Cells produce receptor proteins to detect
these signals and, in turn, to direct downstream cellular responses. Just as
there are many signals, there are many receptors for these signals, and some
receptor genes are in large families. Here, we focus on the embryophyte
receptor family Leucine-Rich Repeat Receptor-Like Kinases (LRR-RLKs).
LRR-RLKs are found in hundreds of copies in embryophyte genomes and
are used as signal receptors for diverse roles in development and defense.
The full extent of this family and its phylogenetic characterization are
critical for functional studies, yet remains incomplete. To address this gap,
we developed an approach for identifying all the members of the LRR-RLK
gene family. Using this approach to search in nine embryophyte genomes,
we found previously unidentified structural variants of LRR-RLKs,
including truncations, conversions, fusions and fissions, and small
duplicated fragments. These structural variants substantially increase the
number of genes in this family and account for ~27% of all genes in our
sampling. Some of these structural variants have been previously classified
into distantly related families, but have strong statistical support as
members of the LRR-RLK family. Gene structural modification in an
important contributor to the evolution of signaling systems and our work
demonstrates that this type of evolution is both an ancient and an ongoing
process. Our results provide a roadmap for better gene detection and
phylogenetic reconstruction in large gene families and could be used for any
gene family.

15
NATURAL VARIATION OF GENE REGULATORY NETWORKS

Arthur Korte, Jan Freudenthal, Ammarah Anwar, William Lopez

University of Wuerzburg, Center for Computational and Theoretical

Biology, Wuerzburg, Germany

Understanding the causal relationship between genotype and phenotype is a

major objective in biology. A default tool to illuminate these relationships
are genome-wide association studies (GWAS). Here the goal is to identfy
genetic loci that associate with the trait of interest. Genomic prediction
(GP), on the other hand, aims to predict the phenotype from the genome.
Both methods have been successfully used in many different species to
elucidate trait architecture or prognose plant response. However, most
studies concentrate on marginal marker effects and ignore epistatic and
gene-environment interactions. These interactions are problematic to
account for, but are likely to make major contributions to many phenotypes
that are not regulated by independent genetic effects, but by more
sophisticated gene-regulatory networks. A further complication arises from
the fact that these networks vary in different natural accessions. Still,
understanding the differences of gene regulatory networks and gene-gene
interactions is crucial to conceive trait architecture and predict phenotypes.
I will present data on statistical aproaches to tackle these challenges and
present examples - using data from the Arabidopsis 1001 Genomes Project
– of gene regulatory networks that have been realized differntly in different
natural accessions.

16
SPATIAL GENETICS OF PLANT COMMUNITIES

Meredith C Schuman1,2, Ewa Czyż1, Cheng Li1, Felix Morsdorf1, Kentaro K

Shimizu3, Bernhard Schmid1,3, Michael E Schaepman1
1
University of Zurich, Department of Geography, Zurich, Switzerland,
2
Max Planck Institute for Chemical Ecology, Molecular Ecology, Jena,
Germany, 3University of Zurich, Department of Evolutionary Biology and
Environmental Studies, Zurich, Switzerland

Spatial genetics is the spatially resolved analysis of heritable traits, their

frequency and distribution in communities, and how this affects adaptation
and community interactions. Spatial genetics research includes approaches
from ecology, remote sensing, chemistry, genetics, and bioinformatics. Our
focus is the spatial genetics of plant-based communities. This is because
plants are the trophic basis of terrestrial ecosystems, and their diversity
structures ecological communities. Specifically, plant genetic and species-
level diversity have large effects, but the mechanisms underlying these
effects are still poorly understood. To understand these mechanisms, and
employ them to achieve e.g. conservation or sustainability goals, and to
improve our projections of future habitats under climate change, we require
a spatially explicit understanding of genetics and chemical signaling in
plant communities. We furthermore require methods for large-scale and
long-term monitoring. Remote sensing technologies can provide
spatiotemporally resolved, large-scale, long-term data.

17
GENE PREDICTION AND CYCLING BEHAVIOR IN SPIRODELA
POLYRHIZA USING FULL-LENGTH cDNA SEQUENCING OVER
DIEL CYCLES

Bradley W Abramson, Nolan Hartwick, Todd Michael

J. Craig Venter Institute, Informatics, La Jolla, CA

While long read nanopore sequencing has ushered in a new era of

contiguous genome assemblies, accurate and complete gene predictions
remain a challenge especially for unique species in underrepresented
regions of the tree of life. Nanopore sequencing enables full length cDNA
(FL-cDNA) sequencing that provides essential empirical evidence of intron-
exon structures and alternative splicing, which compliments ab initio efforts
to define gene models. Here we coupled time-of-day (TOD) sampling with
FL-cDNA sequencing to improve the sensitivity and precision of gene calls
in Duckweed. The Greater Duckweed, Spirodela polyrhiza is re-emerging
as a model plant due to its extremely fast growth rate, aquatic lifestyle,
small genome, minimal set of genes, transformation system, and reduced
body plan. These results highlight the utility of using FL-cDNA to
accurately annotate genomes and determine gene expression patterns.

18
CELL-TYPE SPECIFIC OMICS IDENTIFIES SPATIOTEMPORAL
REGULATION OF PLANT DEVELOPMENT AND PLASTICITY
UNDER INDIVIDUAL AND ABIOTIC STRESS COMBINATIONS.

Amir H Ahkami1, Vimal K Balasubramanian1, Maria D Rubio Wilhelmi4,

Samuel Purvine 1, Lye Meng Markillie 1, Ying Zhu1, Yongil Yong2, Neal
Stewart2, Stephen DiFazio 3, Eduardo Blumwald 4
1
Pacific Northwest National Laboratory (PNNL), Environmental Molecular
Sciences Laboratory (EMSL), Richland, WA, 2University of Tennessee, Plant
Sciences, Knoxville, TN, 3West Virginia University, Biology, Morgantown,
WV, 4University of California, Plant Sciences, Davis, CA

Although global molecular profiling provides a valuable foundation for further

gene and protein functional analyses, understanding complex biological systems
requires characterization of specialized tissue domains and distinct cell-types.
Here we focus on identification of cell-type specific stress-responsive genes and
proteins to provide novel insights into the molecular networks and dynamics
underlying the functions of specific types of cells in poplar tree grown under
individual and combined abiotic stresses. We monitored the response of
Populus tremula x alba clones to water deficit, salinity, heat, and the
combination of all three stresses. While photosynthesis levels and stomatal
conductance were reduced under all stresses, the most significant effect was
observed under drought and combined stress conditions. At three developmental
stages, leaf and root tissues were collected, fixed and embedded for cell-type
specific transcriptome and proteome analyses. We targeted distinct poplar cell
types and tissues including leaf mesophyll, xylem/phloem, and cortex cells
using cryo-sectioning and laser-capture microdissection (LCM) techniques. For
proteomics, total protein was extracted from 300-800 cells per cell-type, and
samples were processed within ultrasmall-volume “nanowells” (nanoPOTS
technology). Focusing on leaf tissue, a total of 4,923 and 6,023 proteins were
identified as palisade mesophyll and vascular-specific proteins, respectively,
under all investigated conditions. Among these, 273 (in palisade cells) and 332
(in vascular cells) proteins were identified as candidate leaf cell-type specific
abiotic stress related-proteins. Focusing on root tissue, a total of 3,475 and
6,845 proteins were identified as cortex and vascular-specific proteins,
respectively, under control, salinity and drought stresses. Among these, 93 (in
cortex cells) and 292 (in vascular cells) proteins were identified as candidate
root cell-type specific abiotic stress related-proteins. Using the PoplarCyc tool,
we identified certain proteins involved in amino acid, carbohydrate, and
secondary metabolism as drought-, salt-, or combined stress-responsive proteins
exclusively in palisade mesophyll or vascular cells. Moreover, to decode the
structural and regulatory gene networks that mediate spatiotemporal
specialization, we employed a cell-type specific gene expression profiling
approach. Our data revealed that under drought, 585 and 138 transcripts were
significantly regulated in leaf palisade and vascular cell types, respectively. This
work provides information that is missing in poplar whole tissue-based
analyses, including cell population-specific protein and gene profiles that are
unique for the distinct cellular layers of leaves and roots.

19
THE FRAGRANT TRAIT (2-ACETYL-1-PYRROLINE): A COMMON
SURVIVAL METABOLITE FROM CROPS TO TREE PLANTS

Siwaret Arikit1, Samart Wanchana2, Apichart Vanavichit1

1
Kasetsart University, Department of Agronomy, Faculty of Agriculture at
Kamphaeng Saen, Nakhon Pathom, Thailand, 2National Science and
Technology Development Agency (NSTDA), National Center for Genetic
Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand

The fragrance contributed by 2-acetyl-1-pyrroline (2AP) is an economically

important trait in several crops including aromatic rice and soybean. The
gene conferring this trait had firstly been identified in rice (OsBADH2) by a
positional cloning and in soybean (GmAMADH2) by a similarity search
approach. The lack of function of the gene is reported contributing to the
2AP biosynthesis in these two crops. The biosynthetic pathway of 2AP is
thought of as a detoxifying mechanism of the agglomerated 4-aminobutanal
in the cells of plants with dysfunctional amino-aldehyde dehydrogenase
(AMADH). To expand our knowledge and provide insights into the
common role of BADH2 in plant evolution, more plant species will need to
be investigated. In this study, we identified the fragrant gene in other crops,
i.e., winter melon, luffa and in tree plants, i.e., coconut and pomelo.
Without a complete genome reference, we identified the gene based on the
de novo assemblies of transcriptomic data. RNA-seq libraries from non-
fragrant and fragrant plants were constructed and sequenced using
Illumina’s HiSeq2500 system. The candidate gene, AMADH2, was
characterized and compared between non-fragrant and fragrant varieties.
Sequence variations identified in the coding regions of AMADH2 in these
plants all suggested the possible role leading to the loss of enzymatic
activity of the AMADH. Our results confirmed that plants share the
orthologous gene and a similar role of 2AP as a common survival
metabolite among plant species.

20
A DYNAMIC MODELING APPROACH TO UNDERSTAND THE
LINKS BETWEEN METAL UPTAKE AND ANTIBIOTIC RESISTANCE
IN PLANTS

Mentewab Ayalew1, Bethany Mwaura1,2, Catherine Rono1, Carla

Kumbale3,4, Eberhard Voit3,4
1
Spelman College, Biology Department, Atlanta, GA, 2Dartmouth College,
Molecular & Cellular Biology Program, Hanover, NH, 3Georgia Institute of
Technology, Department of Biomedical Engineering, Atlanta, GA, 4Emory
University, School of Medicine, Atlanta, GA

Terrestrial plants extract minerals from the soil and in the process may take
up antibiotics that are produced by soil microorganisms. Plants have
evolved resistance mechanisms we are beginning to understand by using a
dynamic modeling approach. In Arabidopsis thaliana, the WBC19 gene
confers resistance to kanamycin but the exact mechanism involved is
unknown. wbc19 mutants are very sensitive to kanamycin and their Zn
uptake is compromised under normal conditions. In addition, Fe uptake in
normal plants declines when they are exposed to kanamycin. These
preliminary findings suggested a complicated link between antibiotics and
the uptake of different metals. In this project, we investigate this link with a
mathematical model that integrates metal homeostasis, especially of Fe and
Zn, with the effects of kanamycin. The proposed model captured the
redundancy as well as the subtle differences between the various
transporters involved in Fe and Zn transport. The dynamic model is
formulated as a Generalized Mass Action (GMA) system and calibrated
with data generated under various experimental conditions. Expanding on
this calibration, large-scale Monte Carlo simulations are performed to
determine ensembles of model instantiations that are consistent with the
experimental results and within biologically acceptable parameter ranges.
The model explains the connection between metal uptake and antibiotic
resistance and illustrates how plants rely on a combination of transporters to
ensure optimal metal uptake. Models such as this are also excellent tools for
introducing undergraduate biology students to quantitative thinking and
thus systems biology. Specifically, they can serve as the basis for hands-on,
computer-aided problem-based exploration and learning.

21
EXPRESSION PATTERNS OF DNA METHYLTRANSFERASES AND
DEMETHYLASES THROUGHOUT PLANT GROWTH AND
DEVELOPMENT AND IN RESPONSE TO PHYTOHORMONES

Morgan Bennett, Kailyn Cleaves, Tarek Hewezi

University of Tennessee, Plant Sciences, Knoxville, TN

Plants are subjected to many biotic and abiotic environmental factors that
hinder growth and development. These stimuli trigger an internal stress
response which precisely and effectively modulates gene expression
through interconnected epigenetic mechanisms. In an attempt to cope with
fluctuating environments, biological processes are ignited and redirected
through the modulation of phytohormones and DNA methylation pathways,
leading to differential expression at thousands of loci. It remains to be
characterized which DNA methylation mechanisms are at play throughout
plant growth and development in various tissues. Thus, we have
characterized the spatial and temporal expression patterns of known
methyltransferases and demethylases involved in de novo DNA
methylation, methyl maintenance, and demethylation in roots, shoots, and
reproductive tissues using GUS reporter systems. It appears that there is
significant de novo DNA methylation and DNA methylation maintenance in
flowers, siliques, and seeds, evident by high levels of expression
DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2).
Overall, DRM2 and DNA METHYLTRANSFERASE 1 (MET1) are the
predominant DNA methyltransferases observed in root tissue. DNA
demethylation is mostly coordinated by DEMETER (DME) these tissues;
however ROS1 is highly expressed in filaments of newly opened flowers. In
shoots, DME and DEMETER-LIKE 2 (DML2) are both highly expressed
DNA demethylases and DRM2 and DRM3 are the primary DNA
methyltransferases. In addition, we treated our GUS reporters with six key
hormones: abscisic acid, ethylene, cytokinin, gibberellin, auxin, and
salicylic acid, and compared gene expression patterns of roots and shoots to
that of the untreated controls. We identified many overlapping and unique
expression patterns. Ultimately, this builds a more comprehensive
understanding of when and where DNA demethylation is happening
throughout plant growth and development and as a result of environmental
stress.

22
SPECIES-SPECIFIC DUPLICATION EVENT CONTROLLING
ADAPTIVE BENEFITS IN SORGHUM BICOLOR IS ONLY
DISCOVERABLE AFTER IMPROVEMENT IN REFERENCE GENOME
QUALITY

Zachary W Brenton1, Elizabeth A Cooper2, Erin L Connolly3, Stephen

Kresovich1
1
Clemson University, Advanced Plant Technology, Clemson, SC,
2
University of North Carolina, Charlotte, Department of Bioinformatics and
Genomics, Charlotte, NC, 3Penn State University, Department of Plant
Science, State College, PA

Sorghum, a highly productive, diverse C4 grass important for both

industrial and subsistence agricultural systems, has considerable phenotypic
diversity in the accumulation of nonstructural sugars in the stem. Besides
economic importance, the accumulation of simple sugars in the stalk has
myriad benefits to plant health and function. Despite the essential nature of
simple sugars in plant biology, many of the biological pathways, signals,
and genetic and biochemical mechanisms remain unknown,
uncharacterized, or at best incomplete. Using a combination of genomic
mapping and comparative genomics, we associate a tandem duplication
event unique to sorghum bicolor with increased sugar content. Additional
sequencing and molecular validation techniques indicate differences in
functionality and suggest possible neofunctionalization. More importantly,
the successful association and subsequent validation of this region was only
possible with improvement of the original reference sequence. The
characterization of this region and the process in which it was discovered
serve as a reminder that any reference genome is imperfect and is in need of
continual improvement. If sorghum, which is known for its high quality
genome, can have mistakes such as these, how much error is in other plant
genomes and how do we design experiments and analyses to account for
mistakes in our references?

23
CHARACTERIZING GENETIC AND TRANSCRIPT VARIATION
USING LONG SINGLE MOLECULE SEQUENCING IN MAIZE

Kapeel Chougule1, Sharon Weix1, Yinping Jiao1, Bo Wang1, Jianing Liu4,

Arun Seetharam3, Shujun Qu3, Brett Hannigan5, Chai Fungtammasan5,
Victor Llaca6, Kevin Fengler6, Candice Hirsch7, Matthew Hufford3, Kelly
Dawe4, Doreen Ware1,2
1
Cold Spring Harbor Laboratory, Ware Lab, Cold Spring Harbor, NY,
2
USDA-ARS-NEA, Robert W. Holley Center for Agriculture and Health,
Ithaca, NY, 3Department of Ecology, Evolution, and Organismal Biology
(EEOB), Iowa State University, Ames, IA, 4University of Georgia,
Department of Plant Biology, Athens, GA, 5DNAnexus, Inc, Mountain
View, CA, 6Corteva Agriscience, Agriculture Division of DowDuPont,
Johnston, IA, 7University of Minnesota, Department of Agronomy and Plant
Genetics, Saint Paul, MN

Maize is both an important crop and genetic model system, with high levels
of genetic and functional diversity. Gene content can vary by more than 5%
across lines, while as much as half of the functional genetic information lies
outside of coding regions in highly variable and repetitive intergenic space.
Characterization of this diversity has been confounded by the reliance of a
single reference genome. Complete and accurate reference genomes from
multiple individuals will be needed to characterize the maize pan-genome,
and to advance the genetic and functional study of this crop. Using PacBio
SMRT sequencing along with high-resolution Bionano optical maps, we
generated reference assemblies, with contig N50 ranging from 6 Mb to 52
Mb, from the 26 parents of the nested association mapping (NAM) founder
lines, which represent a broad cross-section of modern maize diversity. We
are using a standard gene structure annotation protocol and will build gene
trees using the Ensembl compara pipeline, supporting the characterization
of gene space structural variation. While these new technologies have
greatly lowered the cost and improved quality of reference genome
resources, challenges remain in managing and representing data to users.

We gratefully acknowledge funding from NSF award #1744001 and

#1127112.

24
INTEGRATION OF MULTIPLE PROTEOMICS METHODS REVEALS
THE SIGNALING LANDSCAPE OF THE AMPK ORTHOLOG SNRK1
IN PLANTS.

Jelle Van Leene1,2, Astrid Gadeyne1,2, Chao Han1,2, Dominique Eeckhout1,2,

Caroline Matthijs1,2, Nancy De Winne1,2, Geert Persiau1,2, Eveline Van De
Slijke1,2, Geert De Jaeger1,2
1
Ghent University, Plant Biotechnology and Bioinformatics, Ghent,
Belgium, 2VIB, Plant Systems Biology, Ghent, Belgium

Growth and survival of plants requires a well-balanced coordination of

cellular growth with energy and nutrient availability. This metabolic
homeostasis is maintained through complex signaling networks which allow
rapid responses to both internal and external cues. At the heart of these
networks act two evolutionarily conserved, antagonistic protein kinases:
SnRK1, the ortholog of the Mammalian AMPK kinase, is a heterotrimeric
complex that is activated upon energy and nutrient depletion. Upon
activation, SnRK1 triggers a metabolic switch in which catabolic processes
are activated and energy-consuming anabolic processes are repressed. On
the other hand, when growth conditions are favorable, the TOR kinase
promotes growth through activation of anabolic processes. To study TOR
and SnRK1 signaling networks in plants, we initially mapped the signaling
network around the TOR kinase in Arabidopsis. Hereto, we combined
targeted phosphoproteomics with protein complex analysis by affinity
purification coupled to mass spectrometry (AP-MS) (Van Leene et al.,
Nature Plants, 2019), highlighting direct TOR substrates at the intersection
of both datasets. For the phosphoproteomics identification of TOR-
dependent phosphoproteins, sucrose was added - with or without TOR
inhibitors- to sucrose-starved Arabidopsis cell cultures. A more detailed
analysis of the sucrose-dependent phosphoproteins now also uncovered a
large set of novel SnRK1 substrates which were phosphorylated during
sucrose starvation. To shed light on how the heterotrimeric SnRK1 protein
complex is dynamically regulated in plants, we are currently
complementing an extensive SnRK1 AP-MS screen with proximity
labeling, revealing both known as well as novel upstream regulators of
SnRK1, which we are currently studying to reveal their function.
Furthermore, cross-linking mass spectrometry is applied to reveal structural
information and explore dynamic core SnRK1 subunit interactions. Taken
together, the tool box we have built in cell cultures enables to map signaling
networks involving TOR and SnRK1 kinase complexes when nutrients are
limiting. For example, besides sucrose deprivation, we established a proof-
of-concept nitrogen starvation and re-addition protocol for suspension cells
as a basis for in depth signaling analysis. Finally, generating genetics tools
to transfer this knowledge to plants in order to improve plant growth under
limiting nutrient conditions is ongoing.

25
TRANSCRIPTOME ANALYSIS OF SUGARCANE GENOTYPES
CONTRASTING FOR BIOMASS PRODUCTION

Augusto L Diniz1,2, Iago Maiochi3, Monalisa S Carneiro3, Doreen Ware2,4,

Glaucia M Souza1
1
University of São Paulo, Chemistry Institute, São Paulo, Brazil, 2Cold
Spring Harbor Laboratory, Ware Lab, Cold Spring Harbor, NY, 3University
of São Carlos, Department of Biotechnology and Plant and Animal
Production, Araras, Brazil, 4USDA ARS NEA Plant, Soil & Nutrition
Laboratory Research Unit, Ithaca, NY

The interest in bioenergy crops, such as those belonging to the Saccharinae

subtribe, has increased due to improvements in technologies related to the
production of cellulosic ethanol. In this scenario, sugarcane stands out as
one of the world’s leading biomass crop with vast potential to mitigate
climate change effects without affecting food security. The myriad of
products that can derive from sugarcane biomass has been driving breeding
programs towards varieties with a higher yield of fiber and a more vigorous
and rustic performance: the energy cane. In order to obtain genotypes
contrasting for biomass production, we crossed the commercial sugarcane
variety SP80-3280 and IN84-58, a Saccharum spontaneum genotype. Plants
of SP80-3280, IN84-58 and eight interspecific hybrids were planted under
field condition. All genotypes were evaluated for culm height, culm
diameter, stalk number, total biomass production and fiber and sugar
content. In addition, tissue samples from the +1 leaf and upper and maturing
internodes were collected from three biological replicates when the plants
were 4, 8 and 12 months of age. A total of 240 stranded libraries were
prepared and sequenced on Illumina platform to obtain 150 bp paired-end
reads. Clean reads from all samples were aligned to the SP80-3280 gene
space assembly using Hisat2. Preliminary results indicate that 25% of
aligned reads map to intergenic regions, indicating that current SP80-3280
gene annotation might be improved. Nevertheless, it was possible to
quantify the expression levels of over 200,000 genes and Multidimensional
scaling plots and differential expression analysis suggests different
expression patterns when comparing genotypes contrasting for biomass
production. This dataset will be further explored for detecting candidate
genes involved in the regulation of traits of interesting in the energy cane
scenario. We gratefully acknowledge the support from FAPESP grants
2014/50921-8, 2017/02270-6 and 2019/15852-9.

26
IDENTIFYING NOVEL DNA-TRANSCRIPTION FACTOR
INTERACTIONS USING DAP-SEQ

Christina L Ethridge1, Kitra L Cates2, Nathalie G Murphy3, Zefu Lu3,

Robert J Schmitz3
1
University of Georgia, Institute of Bioinformatics, Athens, GA,
2
Washington University in St. Louis, Department of Molecular Genetics
and Genomics, St. Louis, MO, 3University of Georgia, Department of
Genetics, Athens, GA

DNA affinity purification sequencing (DAP-seq) is a novel approach for

studying in vitro interactions between DNA and transcription factors (TFs).
In contrast to ChIP-seq, DAP-seq avoids the use of antibodies specific to
the TF and instead relies on the binding of magnetic beads to a universal
HALO affinity tag fused to the TF of interest. The TF-HALO fusion protein
is incubated with an Illumina NGS-compatible genomic DNA library and
TF-bound DNA fragments are pulled down, purified, and sent for
sequencing. DAP-seq allows for the helical structure of DNA to dictate TF
binding, providing a unique genome-wide characterization of binding
events with distinct advantages over purely computational prediction
methods. Further, DAP-seq data can easily be complemented with in vivo
assays such as ATAC-seq, STARR-seq, and HiChIP-seq to identify putative
cis-regulatory elements (CREs) throughout the genome. This technique
exemplifies an economical, scalable in vitro assay for the massively parallel
identification of TF-DNA binding events in any eukaryotic organism. In a
pilot experiment, we implemented DAP-seq to identify the binding profiles
of 16 Glycine max (soybean) transcription factors. On average, 8,431 peaks
were detected for each TF (0.24% of the genome) and were found to be
enriched at promoters (24.6% within 1kb of transcription start sites). de
novo analyses of DAP-seq peaks identified TF-binding motifs highly
consistent with known motifs of corresponding TFs in Arabidopsis
thaliana. DAP-seq peaks significantly overlapped with accessible
chromatin regions (ACRs) identified by ATAC-seq with 15.25%, 13.98%
and 21.33% of distal, proximal and intragenic ATAC-seq peaks overlapping
at least one DAP-seq peak, respectively. In addition, we have successfully
intersected ATAC-seq, STARR-seq, and HiChIP-seq data with DAP-seq
data to empirically derive CREs in Zea mays (maize). Moving forward, we
plan to characterize genome-wide binding profiles for 300 soybean
transcription factors using DAP-seq in a high-throughput format. DAP-seq
will provide valuable information regarding the binding sites and motifs of
transcription factors, and complemented with other in vivo assays, we can
work to identify putative CREs throughout the genome. With a better
understanding of the interactions between TFs and their target DNA, we can
elucidate the gene regulatory networks that affect a vast array of biological
processes including development, physiology, and stress response.

27
EVOLUTION AND FUNCTION OF DUPLICATE TRANSCRIPTION
FACTOR GENES GT1 AND VRS1 IN MAIZE AND BRACHYPODIUM
DISTACHYON

Joseph P Gallagher1, Harry R Klein1, María Jazmín Abraham Juárez2,

Madelaine E Bartlett1
1
University of Massachusetts, Biology Department, Amherst, MA, 2Instituto
Potosino de Investigación Científica y Tecnológica, División de Biología
Molecular, San Luis Potosi, Mexico

Developmental genes may diverge and evolve new roles following whole
genome duplication (WGD). Class I HD-ZIP transcription factors play a
role in growth repression across the flowering plants, suggesting the
repeated recruitment of these genes to regulate repression. In the grasses,
class I HD-ZIPs GT1 and VRS1 are ancient duplicates and important
domestication genes involved in repressing both reproductive and
vegetative meristems. Here, I ask how these growth repression regulators
evolved following WGD. I hypothesize that WGD has allowed these genes
to be repeatedly recruited for new roles in growth repression. Using both
existing mutants and CRISPR/Cas9-edited lines, I profiled the phenotypes
of gt1 and vrs1 mutants in maize and Brachypodium distachyon
(Brachypodium). These mutants exhibit loss of apical dominance in both
Brachypodium and maize, but also show derepression of floral structures in
maize. I have designed CRISPR/Cas9 guides to dissect promoter regions in
both maize and Brachypodium. Lesions in promoters induced by genome
editing will reveal specific regulatory regions that play a role in shared and
novel functions. Ongoing gene expression and protein localization analyses
will further illuminate how these two gene lineages have diverged following
WGD.

28
CIS-REGULATORY ARCHITECTURE REVEALS POTENTIAL
REGULATORY CIRCUITS INVOLVED IN THE TRANSCRIPTIONAL
REGULATION OF BIP GENES IN POTATO.

Venura Herath1, Mathieu Gayral1, Nirakar Adhikari2, Rita Miller2,

Jeanmarie Verchot1
1
Texas A&M University, Institute for Plant Genomics and Biotechnology,
College Station, TX, 2Oklahoma State University, Department of
Biochemistry and Molecular Biology, Stillwater, OK

Immunoglobulin binding proteins (BiPs) are endoplasmic reticulum (ER)

resident proteins. They are involved in plant development and immune
response. BiPs are the key proteins involved in the ER homeostasis through
their involvement in the unfolded protein response (UPR). Multiple BiP
genes are identified in plant genomes indicating diversification during the
evolution. In this study, we identified three putative BiPs in potato, which
we named as StBiP1, StBiP2 and StBiP3 respectively. StBiPs domain
structures and folding patterns were highly conserved when compared with
other plant BiPs. Phylogenetic analysis revealed that StBiP1 and StBiP2
group with AtBiP1 and AtBiP2 while StBiP3 group with AtBiP3.
Expression analysis of StBiPs showed that StBiP1 and StBiP2 were
ubiquitously expressed in potato. However, StBiP3 expression was highly
induced by salt, heat, and ER stresses. Interestingly, transient expression of
vital proteins induced the expression of all three StBiPs. Finally, we have
identified that cis-regulatory element landscape is playing a major role in
determining the spatiotemporal regulation of BiPs in both Arabidopsis and
Potato. These findings will provide a robust platform towards producing
transgene free and genome-edited climate resilient crops.

29
REDISCOVERY AND FUNCTIONAL CHARACTERIZATION OF THE
CAMV 35S ENHANCER USING STARR-SEQ

Tobias Jores1, Christine Queitsch1, Josh T Cuperus1, Stanley Fields1,2

1
University of Washington, Department of Genome Sciences, Seattle, WA,
2
University of Washington, Department of Medicine, Seattle, WA

With climate change threatening global food security, crop plants with
higher yields and improved response to abiotic stresses are required to
satisfy the needs of our rapidly increasing population. Many beneficial traits
in domesticated crops arose through mutations in enhancers and promoters,
cis-regulatory elements that govern tissue- and condition-specific
expression. Genetic engineering of such elements is a promising strategy for
future crop improvement; however, our knowledge of plant cis-regulatory
elements and their influence on gene expression is limited. To facilitate the
genome-wide identification of active plant regulatory elements, we adapted
STARR-seq – a technology for the high-throughput identification of
enhancers – for its use in transiently transfected tobacco leaves. In a proof-
of-principle experiment, we rediscovered the Cauliflower Mosaic Virus 35S
core enhancer and analyzed the position- and orientation-dependency of its
enhancer activity. While the orientation did not affect the activity of the 35S
enhancer, its location (up- or downstream of the reporter gene) had a strong
effect with the enhancer being more active in the upstream position.
Furthermore, we used saturation mutagenesis analysis to functionally
characterize critical features of the 35S enhancer in the downstream
location. This approach led to the identification of binding sites for
transcription factors such as TCP1 that are relevant for 35S enhancer
activity and to the discovery of novel enhancer variants with increased
strength. The increased enhancer activity could in some cases be attributed
to the introduction of a new transcription factor binding site. However, we
also found enhancer variants with novel motifs that led to increased activity.
These studies establish plant STARR-seq as a feasible experimental avenue
for high-throughput enhancer discovery in crop genomes. Moreover,
saturation mutagenesis of such elements can delineate enhancer features and
identify enhancer variants with altered properties for future genetic
engineering efforts.

30
REIMAGINING HOW PUTRESCINE FUNCTIONS AS A SIGNALING
COMPOUND: THE ESSENTIAL ROLE OF SYNTHESIS,
COMPARTMENTATION, AND TRANSPORT.

Kumud Joshi1, Menaka Ariyaratne1, Sheaza Ahmed1, Andrea Kalinoski2,

Paul F Morris1
1
Bowling Green State University, Biological Sciences, Bowling Green, OH,
2
University of Toledo, Surgery, Toledo, OH

Putrescine is an essential plant metabolite whose synthesis is upregulated in

response to a variety of environmental stresses such as cold, heat, drought
and wounding. In our research, we have revisited how putrescine is
synthesized in the model plant Arabidopsis thaliana and identified two new
biochemical pathways. Here we show that enzymes in these pathways are
restricted to the plastid and the endoplasmic reticulum. Members of the
Brassicaciae have lost ornithine decarboxylase, which mediates the
conversion of ornithine to putrescine, but in both soybeans and rice this
enzyme is also localized to the endoplasmic reticulum. In A. thaliana,
arginine decarboxylase1 (ADC1), agmatine iminohydrolase (AIH), and N-
carbamoylputrescine amidohydrolase (NLP1) mediate a three-step pathway
leading to the synthesis of putrescine. Using transient expression of GFP-
tagged proteins, we show that all of these enzymes are localized to the
endoplasmic reticulum. However, the enzyme At NATA1 is an
acetyltransferase that produces Nδ-acetylornithine from ornithine is also
localized to the ER. In collaboration with others, we recently demonstrated
that AtADC1 can convert Nδ-acetylornithine to acetylputrescine, and its
substrate preference is for Nδ-acetylornithine rather than arginine. A
candidate gene that converts acetyl-putrescine to putrescine has been
identified and is under investigation. AtADC1 and AtADC2 have
overlapping but differential responses to plant stresses and in prior work,
we demonstrated that ADC2 and ARGAH2 provide a third chloroplast-
localized pathway for putrescine synthesis in plants. Finally, we
demonstrate the broad-substrate transporter AtBAT1 can mediate the export
of putrescine from the plastid to the cytoplasm, and present a model that
integrates our present stage of knowledge of putrescine synthesis and
transport in the model plant A. thaliana. This model provides a tool to
address how alterations in polyamine transport can affect fundamental
developmental processes like flowering and drought tolerance.

31
UNDERSTANDING THE EPIGENETIC BASIS OF PLANT NITROGEN
RESPONSE.

Russell S Julian1, Somaiah T Balekuttira2, Shoban K Vimalarani2, Kranthi

Varala1, Ying Li1
1
Purdue University, Horticulture and Landscape Architecture, West
Lafayette, IN, 2Purdue University, Computer Science, West Lafayette, IN

Nitrogen, an essential plant macronutrient, is among the most limiting

factors of crop yield. To sustain modern agriculture, nitrogen is often
amended in soil in the form of chemical nitrogen fertilizer, a major
anthropogenic contributor to nutrient pollution that affects climate,
biodiversity and human health. To achieve agricultural sustainability, a
comprehensive understanding of the regulation of nitrogen response in
plants is required, in order to engineer crops with higher nitrogen use
efficiency. Recently, epigenetic mechanisms have gained increasing
importance as a new layer of regulation of biological processes. However,
how epigenetic processes regulate plant nitrogen response is essentially
unknown, except for one forward genetic screen that links a histone
modification mark with nitrogen response. To fill this knowledge gap, we
combined functional genomics and network inference approaches to
identify a set of nitrogen-responsive epigenetic regulators, and predict their
effects in regulating epigenome and transcriptome during plant nitrogen
response. To do this, we first mined literature to identify all known
Arabidopsis epigenetic regulator proteins, consisted of a total of 286
proteins involved in DNA methylation, histone modification,
nucleosome/chromatin remodeling and siRNA biogenesis. Among them, we
further identified 21 epigenetic regulators that are nitrogen-responsive in
roots, and 29 in shoots, through meta-analysis. Next, a machine learning
network inference approach was used to infer the genome-wide targets of
each of these nitrogen-responsive epigenetic regulators. We hypothesize that
epigenetic modifications of these predicted genomic targets are responsive
to changes in environmental nitrogen levels, which serve as a regulatory
mechanism underlying the global transcriptomic reprogramming during
plant nitrogen response. To test this hypothesis, we focus on four histone
marks: H3K4me3, H3K27ac, H3K27me3 and H3K36me3, based on the
reported biochemical function of the identified epigenetic regulators. We
applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor
the global changes of these epigenetic marks in response to a nitrogen
supply in shoots and roots of tomato plants, followed by RNA-Seq to
profile the transcriptomic changes. These transcriptome and epigenome
datasets will be integrated to gain genome-wide insight into the previously
unknown role of epigenetic processes in plant nitrogen response. The
resulted knowledge will provide a valuable knowledgebase to guide better
design of crops with higher nitrogen use efficiency.

32
MACHINE LEARNING METHOD TOWARDS GENOMIC SELECTION

Joseph K Kawash1,2, Nicholi Vorsa3, Jennifer Johnson-Cicalese3, James J

Polashock2
1
ORISE, USDA-ARS, Chatsworth, NJ, 2USDA-ARS, GIFVL, Chatsworth,
NJ, 3Rutgers University, P.E. Marucci Center, Chatsworth, NJ

Marker assisted selection (MAS) is an invaluable tool utilized in crop

breeding for selection of genotypes and genomic selection (GS). Currently,
most MAS methodologies rely on markers developed from either
quantitative trait loci (QTL) studies or genome wide association (GWAS)
studies. However, there is ongoing research demonstrating that many
phenotypes are not limited to single or few loci easily identified in QTL and
GWAS methods, but often are the result of several small and interacting,
e.g. epistatic, variants of multiple loci. As next generation sequencing,
especially methods such as genotyping by sequencing, becomes more cost
effective for the discovery of increasingly larger proportions of genetic
variation within a population, it becomes more feasible to identify these co-
contributing variations of multiple loci and assess their interactions.
Machine learning (ML) methods offer an alternative method of efficiently
providing informative markers for GS, without the need for highly
structured populations, and an increased ability to identify interacting and
epistatic markers. The use of ML for MAS has been tested in several
agriculturally relevant species including wheat, cattle, and maize. We have
developed methodology that expands on these studies and provides
informative markers for MAS/GS. Our method utilizes genotyping by
sequencing data in common vcf format and a boosted regression trees
algorithm in an easily obtained python package. Results were validated in
several populations of cranberry previously studied for low acid traits,
where highly associated QTL were identified using the R/qtl software
package. In addition, we utilized ML methods to study the polygenic trait of
fruit rot resistance in two populations of cranberry that was not well
characterized using conventional QTL analysis software. Four major
epistatic loci on four different chromosomes were identified in these
populations with three loci contributing to an estimated 23% of phenotypic
variance in one population and two loci contributing to an estimated 27% of
the variance in the remaining population. SNPs at the loci identified
facilitated the creation of rhAmp markers for genotyping and used to screen
seedlings. These markers are now being validated in subsequent breeding
cycles.

33
URI MEDIATES IRON DEFICIENCY SIGNALING IN ARABIDOPSIS
THALIANA

Sun A Kim1, Ian S LaCroix2, Scott A Gerber2,3, Mary Lou Guerinot1

1
Dartmouth College, Department of Biological Sciences, Hanover, NH,
2
Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center,
Lebanon, NH, 3Geisel School of Medicine at Dartmouth, Department of
Molecular and Systems Biology, Lebanon, NH

Iron is an essential nutrient for plants but excess iron is toxic due to its
catalytic role in the formation of hydroxyl radicals. Thus, iron uptake is
highly regulated and induced only under iron deficiency. The mechanisms
of iron uptake in roots are well characterized but less is known about how
plants perceive iron deficiency. Here we show that a basic helix-loop-helix
transcription factor URI (Upstream Regulator of IRT1) acts as an essential
part of the iron deficiency signaling pathway in Arabidopsis thaliana. The
uri mutant is defective in inducing IRT1 and FRO2 and their transcriptional
regulators FIT and bHLH38/39/100/101 in response to iron deficiency.
ChIP-seq revealed the direct binding of URI to the promoters of many iron-
regulated genes including bHLH38/39/100/101 but not FIT. Ectopically
expressing bHLH38/39/100/101 in the uri mutant constitutively activates
the expression of FIT and IRT1, demonstrating that URI determines the iron
deficiency dependent induction of bHLH38/39/100/101. While URI
transcript and protein are expressed regardless of iron status, a
phosphorylated form of the URI protein accumulates only under iron
deficiency. Phosphorylated URI is subject to proteasome-dependent
degradation during iron re-supply and turnover of the phosphorylated form
of URI is dependent on the E3 ligase BTS. The group IVc bHLH
transcription factors, that have previously been shown to regulate
bHLH38/39/100/101, co-IP with URI mainly under Fe deficient conditions,
suggesting it is the phosphorylated form of URI that is capable of forming
heterodimers in vivo. We propose that the phosphorylated form of URI
accumulates under iron deficiency, forms heterodimers with the group IVc
proteins and then induces the transcription of bHLH38/39/100/101. These
transcription factors in turn heterodimerize with FIT and drive the
transcription of IRT1 and FRO2 to increase iron uptake.

34
THE ROLE OF AQUAPORINS IN WATER BALANCE AND
NITROGEN SEQUESTERING

Per O Kjellbom

Lund University, Center for Molecular Protein Science, Division of

Biochemistry & Structural Biology, Lund, Sweden

Aquaporins are water channel proteins of biological membranes, found in

species of all kingdoms. When open, a single aquaporin may be permeable
to 10 to the 9 water molecules per second without allowing any other
molecules to permeate the channel. Transport is passive and can go either
way depending on the concentration gradient across the membrane. In
Arabidopsis thaliana 35 genes encode aquaporin isoforms. Some aquaporins
are abundant and constitutively expressed and some are known to be
temporally and spatially regulated during development and in response to
stress. At a given time, cells express several different aquaporins and it is
likely that aquaporins of plant organelles and of the plasma membrane act
in concert and are responsible for cellular osmoregulation necessary for
maintaining normal metabolic processes. Some aquaporin isoforms are also
known to permeate small uncharged molecules such as glycerol and
ammonia in addition to water. Ammonia-specific aquaporins of the
tonoplast allow the vacuole to rapidly sequester nitrogen and buffer
cytosolic fluctuation of ammonia. Inhibition studies of aquaporins in vivo
and mutant studies suggest that, in addition to cytosolic osmoregulation,
aquaporins are important for the bulk flow of water in plants. Results from
expression profiling of all 35 aquaporin homologues in different
Arabidopsis organs correlate with results from proteomics studies of
membrane fractions from Arabidopsis. Together with the regulated gating
of aquaporins, due to phosphorylation and changes in pH, the localization of
aquaporins in the plasma membrane as well as in organellar membranes
suggest that aquaporins orchestrate not only cytosolic osmoregulation but
also organellar osmoregulation. Aquaporins may therefore also influence
photosynthesis, cellular respiration as well as nitrogen metabolism. The
structure of a water & ammonia specific aquaporin of the plant vacuolar
membrane solved at 1.18 Å resolution will be discussed, in relation to water
balance, nitrogen sequestering and buffering of cytosolic fluctuations of
ammonia.

35
SUGAR SIGNALLING INTERACTS WITH TRANSCRIPTIONAL
REGULATION TO SUPPRESS GROWTH IN MAIZE CARPELS

Harry Klein1, Maria Juarez2, Michelle Heeney3, Edgar Demesa-Arevalo4,

Xiaosa Xu4, Clinton Whipple5, David Jackson4, Madelaine Bartlett1
1
University of Massachusetts Amherst, Biology, Amherst, MA, 2Instituto
Potosino de Investigación Científica y Tecnológica, Molecular Biology, San
Luis Potosí, Mexico, 3Inari Agriculture, Research Associate, Boston, MA,
4
Cold Spring Harbor Laboratory, Plant Biology, Cold Spring Harbor, NY,
5
Brigham Young University, Biology, Provo, UT

Understanding plant development is critical for engineering crops of the

future. One essential process in plant development is growth suppression.
Growth suppression occurs during plant development to sculpt plant
morphology, and in cereal crops, growth is suppressed during inflorescence
development and can affect grain yield. In Zea mays (maize), sex organs are
suppressed during inflorescence development, producing mature
inflorescences with distinct sexual identities. In the male tassel and female
ear, programmed cell death eliminates female organs (carpels) shortly after
initiation. Hormones and transcriptional regulators activate carpel
programmed cell death, but also play other roles in flower development.
One gene that plays a more specific role in carpel programmed cell death is
GRASSY TILLERS1 (GT1) - which suppresses both vegetative growth and
carpel growth in inflorescences. However, carpel growth in gt1 mutant
tassels is only partially derepressed, indicating that other genes act with
GT1 to suppress carpel growth. To identify genes acting with GT1, we
conducted an EMS enhancer screen on gt1 mutants. We identified a mutant
we call rapunzel (rzl) where carpel growth in mutant male flowers is
completely derepressed, and long silks grow out of the tassels. In addition,
carpels in the female ear are derepressed and develop into extra kernels. We
cloned rzl using BSA-Seq, and found that it encodes RAMOSA3 (RA3). RA3
encodes a trehalose-6-phosphate phosphatase (TPP) with roles in
inflorescence determinacy, but no reported roles in floral development. The
gt1 ra3 double mutant provides us with a window into understanding
crosstalk between sugar signalling and transcriptional regulation of growth
suppression in cereal crops.

36
ADVANCING SYSTEMS BIOLOGY OF PLANTS:
TRANSCRIPTOMICS AND GENOME-SCALE METABOLIC
MODELING USING OPEN-SCIENCE COMMUNITY PLATFORM OF
KBASE

Vivek Kumar1, Sunita Kumari1, Doreen Ware1,2, Sam Seaver3, Christopher

Henry3, Bob Cottingham4, Adam Arkin5
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2USDA ARS NEA,
Ithaca, NY, 3Argonne National Laboratory, Argonne, IL, 4Oak Ridge National
Laboratory, Oak Ridge, TN, 5Lawrence Berkeley National Laboratory,
Berkeley, CA

The Department of Energy Systems Biology Knowledgebase (KBase;

http://kbase.us) is an open, web-accessible computational environment for
systems biology research focused on microbes, fungi, plants and their
communities. It provides a range of integrated biological data types and
associated analysis tools (Apps) that include genome assembly and annotation,
gene expression analysis, metabolic modeling, comparative genomics and
microbial community analyses. KBase enables users to upload their data,
perform flexible analyses with a diverse and growing suite of tools, and share
data and analyses with individuals, teams, or publish publicly to the world.
KBase also provides the means for groups to form "Organizations" where they
can share their efforts with each other as teams.

KBase offers a powerful suite of expression analysis tools. Starting with short
reads, the tool suite can be used to assemble and quantify long transcripts,
identify differentially expressed genes, and then cluster and analyze them as
functionally enriched modules. The gene expression values can then be
compared with reaction fluxes when studying metabolic models to identify
metabolic pathways where expression and flux agree or conflict.

KBase also has Apps for the reconstruction, prediction, and design of metabolic
models in microbes and plants. These genome-scale metabolic models can be
used to explore an organism’s growth in specific media conditions, determine
which biochemical pathways are present, optimize the production of an
important metabolite, identify high flux pathways, and more. Plant-specific
compounds and reactions, collected from public sources such as KEGG,
MetaCyc, and AraCyc, have been integrated into PlantSEED and made
available in KBase, where they can be used for plant metabolic modeling. Here
we will demonstrate, through a plant-microbe interactions model in KBase, how
the genome sequences for Sphagnum (peat moss) and an associated microbe are
used to build a combined metabolic model where the plant portion of the model
consumes the nitrogen fixed by the microbial portion of the model.

KBase is funded by the Genomic Science program within the U.S. Department
of Energy, Office of Science, Office of Biological and Environmental Research
under award numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-
AC05-00OR22725, and DE-AC02-98CH10886.

37
VARIATION IN TRANSCRIPTION FACTOR – DNA INTERACTION
IN NATURAL POPULATIONS OF ARABIDOPSIS

Miaomiao Li, Nathaniel Angeles, Shao-shan Carol Huang

Center for Genomics and Systems Biology, Biology, New York, NY

Intraspecific natural variation in plants refers to genetic diversity within a

plant species and provides a valuable source of beneficial traits for plant
breeding. The DNA affinity purification sequencing (DAP-seq) method
provides a high-throughput technique to comparatively analyze multiple
transcription factors (TFs) and their binding sites on population genomes.
Through DAP-seq, we are able to pinpoint TF binding sites across the
entire Arabidopsis genome, as well as to observe the effects of different
genome context and TF variants across accessions. We found several key
TFs controlling circadian rhythm and plant immunity such as LHY1 and
TGA5 showed different binding activities in different genome contexts, and
GO analysis revealed that the target genes were consistent with the binding
variation. In addition, we showed that DAP-seq could identify alteration in
DNA recognition specificities and genome-wide targets by TF variants
found in natural accessions. Collectively, DAP-seq is a powerful tool to
map variation in transcriptional regulatory networks as a result of natural
genome variation.

38
DEVELOPMENT OF SINGLE NUCLEI -OMIC TECHNOLOGIES TO
BETTER UNDERSTAND THE TRANSCRIPTIONAL REGULATION
OF PLANT GENES

Andrew Farmer1, Sandra Thibivilliers2, Ravneet Kaur2, Marc Libault2

1
National Center for Genome Resources, Santa Fe, NM, 2University of
Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, NE

Similar to other complex living organisms, plants are composed of different

and highly specialized cell types (e.g., pollens for plant reproduction, root
hair cells for water and nutrient absorption, etc.). The specific function of
these different cells types is the consequence of the activity of cell-type-
specific genes. The characterization of the expression of these genes is
important to enhance our understanding of plant biology and to ultimately
improve the biological function of specific cell types. Recently, several
groups reported the use of single cell RNA-sequencing (scRNA-seq)
technology on Arabidopsis root protoplasts allowing the identification of
clusters of protoplasts exhibiting the expression profiles of specific
Arabidopsis root cell-types [1-5]. These publications clearly revealed the
power on single cell technologies to precisely reveal the transcriptional
patterns of plant genes. However, using protoplast-based scRNA-seq must
be constantly optimized to notably insure the representation of all the cell-
types composing the plant organs, and to minimize their bursting during the
single cell tagging process. Here, to gain a deeper understanding in the
unique and dynamic regulation of gene expression in and between plant root
cells and cell-types, we developed and applied single nuclei transcriptomic
(snRNA-seq) and epigenomic (snATAC-seq) approaches across different
species including Arabidopsis thaliana and Glycine max. Combining
bioinformatics, molecular, and cellular tools, our analysis revealed plant
root cell-type-specific transcriptional programs, and, in the case of soybean
plants, the transcriptomic programs activated and repressed in root hair cells
in response to rhizobia, nitrogen-fixing bacteria involved in the nodulation
process. We are currently working on merging single nuclei RNA-seq and
ATAC-seq datasets to get a better picture of the regulatory mechanisms of
gene expression required to produce different cell types.

39
SYSTEMS GENETICS ANALYSIS OF WATERLOGGING
TOLERANCE MECHANISMS IN BRASSICA

Jheng-Yang Ou1, Po-Xing Zheng1, Chen-Yu Lin2, Yao-Cheng Lin1

1
Academia Sinica, Agricultural Biotechnology Research Center, Tainan,
Taiwan, 2Taiwan Agricultural Research Institute, Fengshan Tropical
Horticultural Experiment Branch, Kaohsiung, Taiwan

Due to their sessile nature, plants are unable to escape from stressful
environment that prevents the plants from attaining their full genetic
potential for growth and reproduction. Environmental variables, especially
those affecting temperature and water availability, are major determinants
of plant growth and reproduction. Understanding the genetic basis of
phenotypic variations is the central aim in many biological research
questions. Modern bioinformatics and genomics take advantages of high
throughput sequencing that genome sequences and changes of gene
expression values responding to stimuli of non-model organisms can be
measured cost effectively. In this study, we integrate genetics,
bioinformatics and phenomics to help us understanding genes that are
involved in waterlogging stress responses. Using a biparental mapping
population including two parental lines, F1 hybrid and the F2 population,
plant phenotypes including number of leaves, plant height and projected
leaf area were routinely recorded during the growth period. Applying a four
parameter Gompertz growth model, we were able to predict the plant height
inflation point where the plants reach its maximum height and likely shift
from vegetative growth into reproductive growth. Forty days after
transplanting, plants were treated with 48 hours of waterlogging and the
damaged leaf area were scored and gene expression values were measured
by RNAseq. Based on the bulk segregant analysis by integrating gene
expression values and phenotypes, we have identified genes that are
involved in hypoxia responses, photosynthesis and hormone signaling might
play important role in waterlogging tolerance. Our long term goal is to use
these learned knowledge to moving toward precision breeding.

40
MOLECULAR BASIS OF VARIATION IN FLOWERING BEHAVIOUR
IN SCANDINAVIAN POPULATION OF PERENNIAL ARABIS ALPINA

Yi-Chen Lin, Ulla Kemi, George Coupland

Max Planck Institute for Plant Breeding Research, Plant Developmental

Biology, Cologne, Germany

Plants of the same species can have wide-geographical distributions that are
underpinned by adaptation within local populations. Phenotypic variation of
flowering behavior is implicated in adaptation and contributes to
reproductive success and fitness. Regulated by environmental cues such as
day length and vernalization, optimal flowering time in natural populations
confers reproductive success by ensuring that flowering and seed formation
occur at the optimal time. The perennial model species Arabis alpina, a
relative of Arabidopsis thaliana within the Brassicaceae, exhibits variation
in flowering behavior among natural populations ranging from northern
Spain to Norway. My current research centres on the flowering variation
within an A. alpina population in Norway. Several field-collected families
from this population were phenotyped in the glasshouse, where two families
represent early and late-flowering accessions. Without vernalization, the
early accession proceeded to floral bud formation and thereafter produced
an elongated inflorescence on the main shoot. By contrast, under the same
conditions the late-flowering accession proceeded to floral bud formation
but the floral buds remained arrested and the inflorescence did not elongate.
To determine how environmental cues regulate flowering behaviour of both
accessions, different lengths of vernalization period were applied to both
accessions under glasshouse conditions. By applying different lengths of
vernalization, the arrested phenotype in the late accession was rescued and
axillary shoots of both accessions were studied to understand the whole
plant architecture and how this responds to vernalization. Furthermore, to
investigate the genetic basis of the observed phenotypic difference, an
RNA-sequencing experiment was designed to reveal the stage at which
floral development arrests during floral bud development and to identify
sets of genes contributing to this phenotype. By incorporating the results of
RNA-sequencing, phenotypic analysis and ongoing QTL mapping study in
the lab, this research will provide a comprehensive understanding of the
control of flowering behavior by regulating bud arrest within the Norwegian
A. alpina population. Field work will also provide the perspective of
determining the adaptive significance of the observed phenotypic and
genetic variation

41
SCIAPPS.ORG: A CLOUD-BASED PLATFORM FOR SHAREABLE
AND REPRODUCIBLE BIOINFORMATICS WORKFLOWS

Zhenyuan Lu1, Liya Wang1, Peter Van Buren1, Doreen Ware1,2

1
Cold Spring Harbor Laboratory, Ware Lab, Cold Spring Harbor, NY,
2
USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca,
NY

There have been increasing needs to store and analyze data on distributed
storage and computing systems due to the rapid growth of both sequence
and phenotype data generated by high-throughput methods. Meanwhile, a
workflow management system is needed to ensure efficient data
management across heterogeneous systems, simplify the task of analysis
through automation, and make large-scale bioinformatics analysis that could
be easily shared and reproduced. To address these needs, we have
developed SciApps, a cloud-based platform for shareable and reproducible
bioinformatics workflows. The system is integrated with CyVerse Cyber-
infrastructure (CI) through the Tapis platform for job management and
iRODS-based CyVerse Data Store for data management. Each analysis job
is submitted, recorded, and accessed through the web portal and part or all
of a series of recorded jobs can be saved as reproducible, shareable
workflows for future execution using the original or modified inputs and
parameters. The platform is designed to automate the execution of modular
Tapis apps and make it easy to bring reproducible workflows to cloud-based
computing systems. RESTful APIs are also provided for automating large
scale data analysis. Currently we are using SciApps.org to host
MaizeCODE and SorghumBase data.

42
NATURAL AND ENGINEERED ALLELES OF FLM AND FLC
MODULATE FLOWERING TIME IN ARABIDOPSIS THALIANA IN A
CONTINUOUS AND BROAD PHENOTYPIC RANGE

Ulrich Lutz1, Claus Schwechheimer2, Detlef Weigel1

1
Max Planck Institute for Developmental Biology, Department of Molecular
Biology, Tuebingen, Germany, 2Technical University Munich, Plant Systems
Biology, Freising, Germany

The precise timing of flowering is one of the most important factors for a
plant’s reproductive success. Compared to flowering after winter by
vernalization, mechanisms that control spring flowering are less well
understood. Due to global warming, understanding this ambient temperature
pathway has gained much importance. In Arabidopsis thaliana, the MADS-box
transcription factor FLOWERING LOCUS M (FLM) is a critical flowering
regulator of the ambient temperature pathway. We identified insertions in the
first intron of FLM as causative for earlier flowering in many natural
accessions, especially in cool temperatures. By association analysis using FLM
variant data of 800 accessions and expression analysis, regulatory elements
were identified that fine-tune FLM transcript levels and consequently flowering
time in a haplotype-specific and ambient temperature-sensitive manner.
Furthermore, phylogenetic footprinting with six Brassicaceae species identified
two conserved non-coding regions of around 250 bp, which turned out to be
essential for FLM expression. In winter-annual accessions effects of FLM and
other flowering time regulators are often masked by the vernalization gene
FLOWERING LOCUS C (FLC), which is downregulated during a long cold
period. To unmask effects of known as well as yet unidentified flowering time
alleles a CRISPR/Cas9 approach was applied to generate artificial genomic
deletions of FLC (ΔFLC) in 85 winter-annual A. thaliana accessions. Flowering
time was assessed in 2 to 4 independent T3 lines per accession in long days.
There is surprisingly large phenotypic variation in ΔFLC lines, which flowered
from 11 to 50 days after germination (4 to 45 true leaves) translating into
acceleration of flowering from 8 to 75%. However, only a low correlation
between the effect size and flowering of the wild type was found. Together,
these preliminary results indicate an important contribution of FLC-independent
pathways to the delay of flowering. Analysis of whole genome sequencing data
of all T3 lines (total 280) is on the way and will especially focus on off-target
mutations. This new biological resource will also be exploited for GxG
interaction and investigation of phenotypic pleiotropy of FLC. Such new
knowledge about gene regulatory regions and their phenotypic effects, FLC-
masked alleles, and genetic interactions may serve as an example how flowering
time and several other pleiotropic controlled phenotypes can be fine-tuned using
either natural alleles mined from standing variation of natural resources or
artificially constructed alleles generated by CRISPR-Cas to dynamically adapt
agricultural systems, e.g. to buffer the anticipated negative effects of climate
change.

43
DISSECTING THE GENE REGULATORY NETWORK CONTROLLING
PHENOLIC BIOSYNTHESIS IN MAIZE USING TRANSCRIPTION
FACTOR MUTANTS

Erika Magnusson1, Peng Zhou1, Peter Hermanson1, Yi-Hsuan Chu2, Lina

Gomez2, Andrea Doseff3, Natalia De Leon4, John Gray5, Candice Hirsch6,
Erich Grotewold2, Nathan Springer1
1
University of Minnesota, Plant and Microbial Biology, St. Paul, MN,
2
Michigan State University, Biochemistry and Molecular Biology, East
Lansing, MI, 3Michigan State University, Physiology, East Lansing, MI,
4
University of Wisconsin-Madison, Agronomy, Madison, WI, 5University
of Toledo, Biological Sciences, Toledo, OH, 6University of Minnesota,
Agronomy and Plant Genetics, St. Paul, MN

Transcription factors (TFs) represent only 5-10% of the maize coding

genome, but in large part control transcription of all protein-coding genes.
A single TF or a discrete number of TFs exhibiting combinatorial control
can regulate multiple structural genes within biosynthetic pathways, making
them attractive targets for control of key metabolites. However, of the over
~2000 TFs predicted in maize only a handful have been functionally
characterized and linked to target genes and their metabolic output. Here we
focus on the maize phenolic biosynthesis pathway, as pathway enzymes are
well-characterized and specialized metabolites produced (general
phenylpropanoids, flavonoids and lignins) are important for maize crop
productivity. Prior research utilized a yeast one-hybrid screen to identify a
set of 45 TFs that interact with promoters of multiple maize phenolic
biosynthesis genes. We have collected putative loss-of-function alleles for
these genes from available sequence indexed resources. These alleles were
used for genotyping, back-crossing and characterization resulting in
segregating alleles for 20 of the 45 TF genes. Expression analysis confirms
loss of transcript expression or altered transcript structure for many alleles
with exon insertions, but few alleles with UTR or intron insertions.
Phenotypic effects of TF loss-of-function alleles were assayed with
morphological trait measurements related to changes in lignin composition
and metabolite profiling to detect qualitative and quantitative changes of
phenolics. To determine these TFs in vivo functional targets and their
regulation, expression profiling for TF mutants will be combined with
ChIPseq and DAPseq TF binding site data. Overlaying potential TF binding
sites with transcript profiling in TF mutants has the power to elucidate TF-
target interactions on a genome-wide scale and identify putative direct and
indirect targets. Together, these data will provide insights into whether and
how perturbation in TFs translate to metabolic networks. By focusing on
multiple TFs at a time, we hope to resolve the hierarchical regulatory
relationships among pathway members involved in phenolic biosynthesis.

44
DOUBLE TRIAGE TO IDENTIFY POORLY ANNOTATED GENES IN
MAIZE

Cristina F Marco*1, Marcela K Tello-Ruiz*2, Fei-Man Hsu3, Rajdeep S

Khangura4, Pengfei Qiao5, Sirjan Sapkota6, Michelle C Stitzer7, Rachael
Wasikowski8, Hao Wu9, Junpeng Zhan10, Kapeel Chougule2, Lindsay C
Barone1, Cornel Ghiban1, Demitri Muna2, Andrew Olson2, Liya Liya 2,
Doreen Ware1, David A Micklos1
1
Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring
Harbor, NY, 2Cold Spring Harbor Laboratory, Plant Biology Program, Cold
Spring Harbor, NY, 3University of Tokyo, Graduate School of Frontier
Sciences, Chiba, Japan, 4Purdue University, Biochemistry, West Lafayette,
IN, 5Cornell University, Plant Biology Section, Ithaca, NY, 6Clemson
University, Plant and Environmental Sciences, Clemson, SC, 7University of
California, Plant Sciences and Center for Population Biology, Davis, CA,
8
University of Toledo, Biological Sciences, Toledo, OH, 9Iowa State
University, Genetics, Development & Cell Biology, Ames, IA, 10Donald
Danforth, Plant Science Center, St. Louis, MO

As genome sequencing becomes cheaper and faster, biologists rely on

automated systems to predict genes and to annotate their structure and
function. The sophistication of gene prediction algorithms and the
abundance of RNA-based evidence for the maize genome may suggest that
manual curation of gene models is no longer necessary. To evaluate the
efficiency of one of those automated gene prediction pipelines, MAKER-P,
we tested a two-part system to identify poor-quality gene annotations in
maize: Quality metrics generated by MAKER-P and the Gramene gene tree
visualizer. Quality metrics were used to mathematically determine how well
a gene structure is supported by independent experimental evidence, while
the gene tree visualizer was used to inspect how well coding and noncoding
components align among related genes. Working with eight graduate
students, we used the Apollo annotation editor to curate a subset of classical
transcript models flagged by both MAKER-P quality metrics and the
Gramene gene tree visualizer. All of the triaged models had significant
errors – including missing or extra exons, non-canonical splice sites, and
incorrect UTRs. A correct transcript model existed for about 60% of genes
(or transcripts) flagged by quality metrics; we attribute this to the
convention of selecting the transcript with the longest coding sequence
(CDS) to the canonical, or first, position. The remaining 40% of flagged
genes resulted in novel annotations and represent a manual curation space
of about 10% of the maize genome (~4,000 protein coding genes). Together
with the Apollo graphical editor, our double triage provides an
infrastructure to support the community curation of eukaryotic genomes by
scientists, students, and potentially even citizen scientists.

45
POST-GENETIC RESPONSES TO PHOSPHATE STARVATION AND
HEAT STRESS IN ARABIDOPSIS THALIANA

Devang Mehta1, Luc Cornet2, Syed S Ali2, Maria Rodriguez1, Matthias

Hirsch-Hoffmann3, Mina Ghahrehmani4, María Pérez-Fernández5, William
C Plaxton4, Hervé Vanderschuren2,6, R. Glen Uhrig1
1
University of Alberta, Biological Sciences, Edmonton, Canada, 2University
of Liège, Gembloux Agro-Biotech, Gembloux, Belgium, 3University of
Zurich, Hospital of Psychiatry, Zürich, Switzerland, 4Queen's University,
Biology, Kingston, Canada, 5Pablo de Olavide University, Physical,
Chemical and Natural Systems, Seville, Spain, 6KU Leuven, Bioscience
Engineering, Leuven, Belgium

Over the last thirty years, several molecular events operating on the
products of the central dogma processes of DNA replication, transcription
and translation have been found to play an important role in controlling
gene regulation in a rapid, adaptive and responsive manner to various
external stimuli. Here, I will present work on two projects investigating the
role of three such processes: RNA splicing, protein phosphorylation, and
extra-chromosomal DNA (eccDNA) production, in Arabidopsis plants
subject to phosphate starvation and heat stress. Using quantitative
proteomics and phospho-proteomics we have discovered that
phosphorylation of RNA splicing factors is an important signature of the
plant response to phosphate starvation and are currently carrying out
targeted studies into potential phospho-switches guiding plant gene
regulation in response to phosphate and phosphite treatment. We are also
carrying out pioneering biochemical assays of spliceosome activity in plants
and attempting to elucidate changes in spliceosome composition during
stress. In a second study, I am investigating the presence of eccDNA
molecules in Arabidopsis plants suffering from heat stress using a newly
developed method for sequencing eccDNA. This method called CIDER-Seq
leverages the power of third-generation long-read sequencing to produce
accurate sequences of eccDNA molecules without computational sequence
assembly. Collectively, these proteomics and genomics-technology driven
experiments point towards an important role for genome plasticity and post-
genetic regulation in plant responses to future challenges to agriculture such
as rising temperatures and declining phosphate fertilizer supply.

46
ANNOTATION OF THE TUB TRANSCRIPTION GENE FAMILY IN
ZEA MAYS

Sendi Meja1,2, Marcela Karey Tello-Ruiz2, Cristina Fernandez-Marco2,

Doreen Ware1,3, Christos Noutsos1
1
SUNY College Old Westbury, Biology, Old Westbury, NY, 2Cold Spring
Harbor Laboratory, Ware, Cold Spring Harbor, NY, 3USDA ARS NEA
Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY

TUB transcriptions factors are well conserved between animals and plants.
In animals, they play a role in neuronal cells. In plants, they might play a
role in ABA signaling. In this work, we have used the 10 TUB genes from
Arabidopsis thaliana to idendify the homologues in Zea Mays version 4. In
total we found 14 homologues belonging to the TUB family. In Zea mays
the homologs are present in chromosomes 1 to 9. There is no TUB gene in
chromosome 10. This is a totally different organization compared with
Arabidosis thaliana, where the majority of the 10 TUB genes are in
chromosome 1. The next step was to use the online version of Apollo to
correct the automatic gene annotation for the TUB genes. The manual
annotation was based on RNA-Seq data in different developmental stages as
well as PacBio Long Reads. A lot of the alternative spliced mRNA models
were not supported from the data and we had to delete them and in 10
primary mRNAs we had to correct the models. Finally, we performed RT-
PCRs for all TUB Transcription Factors as well as in the alternatively
spliced products using cDNA to validate the structures we have corrected

47
IDENTIFICATION OF lncRNAs BY UTILIZATION OF HISTONE
MODIFICATION DATA IN ZEA MAYS

John P Mendieta1, William A Ricci2, Robert J Schmitz1

1
University of Georgia, Genetics, Athens, GA, 2University of Georgia, Plant
Biology, Athens, GA

lncRNAs remain a difficult and elusive class of genes to study in plant

genomes. Generally, lncRNAs are missed during annotation due to their
recent evolutionary history, lack of homology to any known sequence, and
similarity to in-silico artifacts generated during transcriptome assembly.
This lack of accurate lncRNA annotations is a pressing issue as lncRNAs
have been implicated as major players in gene regulation. lncRNA have
been shown to modify local chromatin environments by way of recruiting
chromatin remodeling complexes, as well altering 3D genome interactions
by means of stabilizing loops. Without accurate lncRNA annotations, the
field stands to potentially miss an important class of genes responsible for
major changes in gene expression. Chromatin data in the form of ChIP-seq
offers an immediate method in which to supplement and refine current
lncRNA annotations and ameliorate many of these issues. Chromatin is
comprised of dynamic histone proteins that not only condense and package
DNA, but also modulates DNA accessibility by various chemical
modifications appended to the alpha globulin tail of the histone octamer. By
utilizing histone modifications known to correlate with transcriptional
elongation (H3K36me3 and H3K4me1), as well as modifications critical for
the recruitment of Pol II (H3K4me3 and H3K56ac), we are able to
accurately identify novel transcripts, while avoiding challenges associated
with the spurious nature of transcription. Upon utilization of chromatin data
in the genomes of Zea mays, we identified over ~400 novel transcripts in a
single tissue. As a byproduct of this method, we also identified~ 200 mis-
annotated gene models that required merger, as well as an additional ~1,000
gene models that required extension. These results demonstrate that
chromatin modification data can act as an efficient method to identify novel
genes, while providing the added benefit of enhancing current genome
annotations. The annotation of these lncRNAs provided the foundation for
further research exploring the relationship between lncRNAs and their
protein coding gene, as well as to their overlap with distal cis regulatory
elements.

48
A TRANSPORTER FOR DELIVERING ZN TO THE DEVELOPING
TILLER BUD IN RICE

Shuai Mu1,2, Mary L Guerinot2, Luqing Zheng1

1
College of Life Sciences, Nanjing Agricultural University, Nanjing, China,
2
Department of Biological Sciences, Dartmouth College, Hanover, NH

Tillering in rice is one of the most important agronomic traits that determine
grain yields. Development of the axillary meristems (AM) with low
transpiration rates requires high zinc (Zn) levels for the active growth of the
tiller bud, but the underlying molecular mechanisms by which Zn is
delivered are poorly understood. Using rice tiller buds, we performed an in-
depth temporal transcriptome analysis. OsZIP4, a member of the ZIP (ZRT,
IRT-like protein) gene family, showed the highest expression level among
all ZIP genes; its expression gradually increased with Zn deficiency but
rapidly decreased when Zn was re-supplied. Immunostaining analysis
confirmed the high expression level of OsZIP4 in AM at the tillering stage.
At the vegetative stage, OsZIP4 was expressed in the phloem region of both
the diffuse vascular bundles (DVBs) and the enlarged vascular bundles
(EVBs) in node I. Knockout of OsZIP4 resulted in a significant decrease in
development of the young leaf and tiller buds, but an increase in Zn
concentration in the shoot basal stem. Zn concentrations were lower in the
AM of the tiller during the tillering stage in the knockout lines as compared
with wild-type rice. Using micro x-ray fluorescence (μ-XRF) scanning, Zn
levels tended to be higher in the EVBs and transit vascular bundles (TVBs)
in the shoot basal stem in the mutant line compared to wild-type at the
tillering stage. In summary, OsZIP4 is responsible for transporting Zn from
the phloem of EVBs to the youngest meristems, which plays an important
role in preferential distribution of Zn to the developing tiller bud in rice.

Keywords: zinc, ZIP, transporter, distribution, the basal stem, tiller bud,
AM, rice

49
CHARACTERIZATION OF THE GENOME STRUCTURE OF AN
ESSENTIAL OIL PLANT, LAVENDER (LAVANDULA
ANGUSTIFOLIA).

Radesh Nattamai Malli Pooranachandhiran1, Calvin Sjaarda2, Robert

Baldwin2, Soheil Mahmoud3, Ping Liang1,2
1
Brock University, Centre for Biotechnology, St.Catharines, Canada, 2Brock
University, Department of Biological Sciences, St.Catharines, Canada,
3
University of British Columbia, Department of Biology, Kelowna, Canada

Lavender (Lavandula angustifolia) is a perennial plant native to the

Mediterranean region and is best known for its essential oil (EOs) that has
numerous applications in the pharmaceutical, cosmetic and perfume
industries. We have recently sequenced the L. angustifolia genome. Here,
we report a detailed analysis of this highly duplicated and complex genome,
focusing on genome size, ploidy, and repeat content. The lavender genome
was estimated to be around 870 Mbp (1C=0.96 pg) using a quantitative
PCR method. Genome size was further validated through analysis of raw
genome sequences using Kmergenie, providing a conclusive end to the
lavender genome size dispute. The repeat element composition of the
genome was identified using de novo (RepeatModeler) and also library-
based methods (RepeatMasker) and was estimated to be around 45% of the
full genome or ~57% of the non-gap genome sequences. Further
characterization revealed Long Terminal Repeat (LTRs) retrotransposons as
the major repeat component, which contributes to ~18% of the genome,
followed by DNA transposons at ~8.5% of the genome. Interestingly, unlike
most other plant genomes, the lavender genome has much more Copia than
Gypsy elements, both showing a trend of recent increasing activity.
Furthermore, these LTRs, especially Copia, have shown active participation
in gene function including genes for essential oil production, with Copia
elements contributing to ~30 % of the CDS regions, in addition to promoter,
intron and UTR regions. The lavender genome also has an unusually high
number of miniature inverted-repeat transposable elements (MITEs)
compared to other model plant genomes, with the number being ~88,000,
which is close to that of the maize genome (~90,000) that is double in size.
Analysis also revealed the lavender genome with a high proportion at
polyploidy level, which is strongly biased towards regions containing
essential oil genes. Analysis of Ks substitution rates estimated the
occurrences of polyploidization events in the lavender genome to be
between 16 to 41 Mya, which may be partially responsible for the presence
of high copy numbers of EO genes in the genome likely by selective gene
retaining favouring EO genes during later evolution of the polyploid
genome. In conclusion, our results reveal the lavender genome to be highly
duplicated and with past and ongoing active retrotransposition, favouring
EO production.

50
IDENTIFICATION OF A ROLE FOR GMKIX1 IN REGULATING
ORGAN SIZE IN SOYBEAN

Cuong X Nguyen, Kyle J Paddock, Zhanyuan Zhang, Minviluz G Stacey

University of Missouri-Columbia, Division of Plant Sciences, Columbia,

MO

Seed weight is one of the most important agronomic traits in soybean for
yield improvement and food production. Several quantitative trait loci
(QTLs) associated with the trait have been identified in soybean; however,
the genes underlying the QTLs and their functions remain largely unknown.
Using forward genetic methods and CRISPR/Cas9 gene editing system, we
identified and characterized the role of GmKIX1in the control of organ size
in soybean. GmKIX1 belongs to a family of KIX domain-containing
proteins that negatively regulates cell proliferation in plants. Consistent
with this predicted function, we found that loss-of-function GmKIX1
mutants showed a significant increase in the size of aerial plant organs such
as seeds and leaves. Likewise, the increase in organ size is due to increased
cell proliferation, rather than cell expansion, and increased expression of
CYCLIN D3;1-10. Lastly, molecular analysis of soybean germplasms
harboring the qSw17-1 QTL for big-seeded phenotype indicated that
mutations in GmKIX1 is the genetic basis of the qSw17-1 phenotype.

51
RNA POL4 MEDIATES DIVERGENT MATERNAL AND PATERNAL
IMPACTS ON THE ARABIDOPSIS ENDOSPERM.

Satyaki P RV, Mary Gehring

Whitehead Institute for Biomedical Research, Gehring Lab, Cambridge,

MA

Endosperm is a placental tissue found in seeds that mediates nutrient

transfer from the mother to the growing seed. It is a key tissue both
economically and ecologically as it comprises the bulk of the edible
portions of seeds from all flowering plants including cereals and oil seeds. It
is also a proposed site for parental conflict. However, beyond lists of
imprinted genes and a handful of seed phenotypes associated with mutation
of imprinted genes there is little molecular evidence for parental conflict.
RNA Pol IV is necessary for the biogenesis of sRNAs that direct DNA
methylation in the RNA directed DNA methylation pathway. I observed
that paternal RNA PolIV loss represses paternal excess seed abortion while
maternal RNA Pol IV loss enhances paternal excess seed abortion. I tested
the basis for these divergent parental effects by profiling endosperm
transcriptomes from heterozygous pol iv seed where the mutant allele was
inherited from either the mother or the father. Strikingly, I found that genes
that enhance endosperm growth are upregulated by loss of maternal Pol IV
and down-regulated by loss of paternal Pol IV. These results strongly
support the parental conflict model.

52
GENOME-WIDE ASSOCIATION MAPPING AND
CHARACTERIZATION OF CANDIDATE GENES CONTROLLING
DIRTY PANICLE DISEASE RESISTANCE

Kanamon Riangwong1, Theerayut Toojinda2, Samart Wanchana2, Meechai

Siangliw2, Siwaret Arikit3, Jintana Unartngam4
1
Interdisciplinary Graduate Program in Genetic Engineering, Graduate
School, Kasetsart University, Bangkok, Thailand, 2National Center of
Genetic Engineering and Biotechnology (BIOTEC), National Science and
Technology Development Agency (NSTDA), PathumThani, Thailand,
3
Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen and
Rice Science Center, Kasetsart University, Nakhon Pathom, Thailand,
4
Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen
and Rice Science Center, Kasetsart University, Nakhon Pathom, Thailand

Rice (Oryza sativa L.) is a staple food feeding for more than half of the
world’s population. Rice production is affected by many diseases affecting
the rice yield resulted in yield losses. Particularly, dirty panicle disease is an
emerging disease for rice production areas in Thailand which is repeatedly
found in most of the rice-growing areas throughout the country. The disease
damages rice yield and also reduces seed and grain quality. The major
pathogen agents causing dirty panicle disease include Curvularia lunata,
Cercospora oryzae, Bipolaris oryzae, Fusarium semitectum, Trichoconis
padwickii and Sarocladium oryzae. At present, there has not been reported
about the identification and mapping of rice dirty panicle disease resistance
gene/QTL. In this study, we identified the candidate regions in the rice
genome associated with the dirty panicle caused by Bipolaris oryzae and
Curvularia lunata using a genome-wide association study (GWAS)
approach based on 264 varieties of rice and about two hundred thousands of
SNPs. Using a linear mixed model with correction of kinship bias and
population structure, we identified candidate regions for dirty panicle
disease on chromosomes 2, 4 and 5. We found some disease resistance
genes such as protein kinase, nitrate-induced NOI protein, leucine-rich
repeat family protein, disease resistance RPP13-like protein 1 and disease
resistance protein RGA2 within these regions. The future research is to
identify the candidate genes within the detected regions and further develop
DNA markers for marker-assisted selection in breeding programs.

53
THE VE-RESISTANCE LOCUS IN TOMATO, A PLANT SIGNALLING
INTERCEPT

Jane Robb1, Hakeem O Shittu1, Christian D Castroverde1, Xin Xu1,

Alexander Kurosky2, Ross N Nazar1
1
University of Guelph, Molecular and Cellular Biology, Guelph, Canada,
2
University of Texas, Medical Branch, Galveston, TX

Signalling crosstalk in plants has been recognized for several decades but
the manner in which these interactions occur continues to pose many
questions. Examples of crosstalk between plant defense responses and
growth have been recognized but little is known about receptors that may be
shared in this crosstalk. In tomato, resistance to Verticillium dahliae and V.
albo-atrum, race 1 has been attributed to the Ve-resistance locus,
comprising two closely related back-to-back genes, Ve1 and Ve2. Both
appear to encode plasma membrane receptor proteins. Ve1 gene expression
is induced and Ve2 is constitutive. Recent studies in our laboratories have
shown that Ve2 controls the expression of the defense cascade, which
appears to contribute to symptom development, while induction of Ve1
promotes root growth, which permits the plant to lower the concentration of
Verticillium by outgrowing the fungus. Furthermore, proteomic analyses
indicate that the two receptor proteins act antagonistically, the induction of
Ve1 also causing a down regulation of Ve2 gene expression and a
subsequent reduction in defense protein levels. These observations suggest
strongly that the Ve-locus is a signaling intercept. Alternate models for the
antagonistic effects are compared and discussed.

54
DIVERSITY OF MYB TRANSCRIPTION FACTORS ACROSS APPLE,
GRAPE AND KIWIFRUIT GENOMES

Jessica A Rodrigues1, Richard V Espley1, Andrew C Allan1,2

1
New Zealand Institute for Plant & Food Research Ltd, Mt Albert Research
Centre, Auckland, New Zealand, 2University of Auckland, School of
Biological Sciences, Auckland, New Zealand

MYB transcription factors regulate a wide variety of developmental and

metabolic processes in plants. They affect plant characteristics ranging from
stress tolerance, organ patterning, and reproductive viability, to colour,
flavour, and the production of bioactive compounds. Updated genome
assemblies1-3 and increased access to diverse RNA-seq data have allowed us
to identify novel MYB genes in apple, grape and kiwifruit genomes. Taking
advantage of these novel MYB genes, prior characterization of MYBs in
other species4, and recent advances in phylogenetic methods5-8, we provide
support for revising the relatedness and membership of some previously-
defined MYB subgroups4,9. We also identify MYB genes that appear to be
regulated by antisense transcripts and intron retention. To demonstrate the
relevance of our approach to fruit trait enhancement, we showcase novel
findings pertaining to the production of anthocyanin pigments, which
impart red and blue hues to fruit.

1. Daccord N et al. 2017. High-quality de novo assembly of the apple genome

and methylome dynamics of early fruit development. Nature Genetics 49: 1099-
1106.
2. Canaguier A et al. 2017. A new version of the grapevine reference genome
assembly (12X.v2) and of its annotation (VCost.v3). Genomics Data 14: 56-62.
3. Pilkington SM et al. 2018. A manually annotated Actinidia chinensis var.
chinensis (kiwifruit) genome highlights the challenges associated with draft
genomes and gene prediction in plants. BMC Genomics 19: 257.
4. Du H et al. 2015. The evolutionary history of R2R3-MYB proteins across 50
eukaryotes: New insights into subfamily classification and expansion. Scientific
Reports 5: 11037.
5. Nguyen LT et al. 2015. IQ-TREE: A fast and effective stochastic algorithm
for estimating maximum-likelihood phylogenies. Molecular Biology and
Evolution 32: 268-274.
6. Chernomor O, von Haeseler A, Minh BQ 2016. Terrace aware data structure
for phylogenomic inference from supermatrices. Systematic Biology 65: 997-
1008.
7. Kalyaanamoorthy S et al. 2017. ModelFinder: Fast model selection for
accurate phylogenetic estimates. Nature Methods 14: 587-589.
8. Hoang DT et al. 2018. UFBoot2: Improving the ultrafast bootstrap
approximation. Molecular Biology and Evolution 35: 518-522.
9. Dubos C et al. 2010. MYB transcription factors in Arabidopsis. Trends in
Plant Science 15: 573-581.

55
DISTINCT EVOLUTIONARY ORIGINS OF INTRON RETENTION
SPLICING EVENTS IN NHX1 ANTIPORTER TRANSCRIPTS RELATE
TO SEQUENCE SPECIFIC DISTINCTIONS IN ORYZA SPECIES

Gothandapani Sellamuthu 1, Vidya Jegadeeson1, Radha S Sajeevan2, Raja

Rajakani1, Pavithra Parthasarathy1, Lana Shabala3, Zhong-Hua Chen4,
Meixue Zhou3, R Sowdhamini2, Sergey Shabala3, Gayatri Venkataraman1
1
M.S. Swaminathan Research Foundation, Biotechnology, Chennai, India,
2
National Centre for Biological Sciences, Bioinformatics, Bangalore, India,
3
University of Tasmania, Tasmanian Institute of Agriculture, College of
Science and Engineering, Hobart, Australia, 4Western Sydney University,
School of Science and Health, Hawkesbury Institute for the Environment,
Penrith, Australia

The genome of Asian cultivated rice (Oryza sativa L.) shows the presence
of six organelle-specific and one plasma membrane (OsNHX1-7) NHX-type
cation proton antiporters. Of these, vacuolar-localized OsNHX1 is
extensively characterized. The genus Oryza consists of 27 species and 11
genome-types, with cultivated rice, diploid O. sativa, being an AA-type
genome. Oryza NHX1 orthologous regions [gene organization, 5' upstream
cis elements, amino acid residues/motifs] from closely related Oryza AA
genomes cluster distinctly from NHX1 regions from more ancestral Oryza
BB, FF and KKLL genomes. These sequence-specific distinctions also
extend to two separate intron retention (IR) events involving Oryza NHX1
transcripts that occur at the 5' and 3' ends of the NHX1 transcripts
respectively. We demonstrate that the IR event involving the 5' UTR is
present only in more recently evolved Oryza AA genomes while the IR
event governing retention of the 13th intron of Oryza NHX1 (terminal
intron) is more ancient in origin, also occurring in halophytic wild rice
Oryza coarctata (KKLL). We also report presence of a retro-copy of the
OcNHX1 cDNA in the genome of O. coarctata (rOcNHX1). Preferential
species and tissue specific up- or down-regulation of the correctly spliced
NHX1 transcript/ 5' UTR/13th intron-retaining splice variants under salinity
is observed. The implications of IR on NHX1 mRNA stability and ORF
diversity in Oryza spp. is discussed.

56
TRANSGENIC TOBACCO PLANTS AS A TOOL FOR CORRECT
HYDROXYLATION AND SYNTHESIS OF HUMAN COLLAGEN
PEPTIDES

Yana Sindarovska, Maksym Vasylenko, Mykola Kuchuk

Institute of Cell Biology and Genetic Engineering NASU, Genetic

Engineering, Kyiv, Ukraine

Collagen is the main structural protein of connective tissues, and it is an

important biomaterial with a lot of medical applications. Collagen
production in plants has both advantages (low cost, large scale etc.) and
limitations (e.g., lack of prolyl-4-hydroxylase (P4H) enzyme). To overcome
the problem, genes encoding P4H and collagen peptides must be expressed
in plant simultaneously. There are two common ways for foreign protein
production in plants: via transient or stable gene expression. Transient gene
expression (TGE) allows fast obtaining of high amounts of recombinant
proteins, while transgenic plants transmit target gene to their offspring. To
improve collagen production, two strategies were combined: obtaining
transgenic plants carrying p4h gene and further using these plants for
Agrobacterium-mediated TGE. Earlier, transgenic Nicotiana benthamiana
(Australian tobacco) plants carrying the p4h(α) gene were generated by
agro-transformation. Seeds from self-pollinated transgenic plants were
taken for further analysis. Seedlings were grown under selective pressure,
and resistant plants were analyzed for the presence of p4h gene. Confirmed
transgenic T1 plants were transferred in greenhouse conditions, and then
were tested as hosts for recombinant protein production. For this task GFP
was chosen as a reporter protein. Different transgenic lines and various
genetic construction carrying gfp gene were tested. Offspring of some p4h
transgenic lines demonstrated altered branchy phenotype, thus providing
more available leaf biomass for protein production per one plant. The
brightest fluorescence indicating on very high GFP accumulation was
observed when viral-based constructions were used, especially with PVX-
based one. Systemic GFP distribution was detected after few days on the
plants infected with PVX-based genetic construction, and bright
fluorescence was visible in stems and young green leaves while initial
infiltration sites were necrotic. Typically, using of viral constructions leads
to maximal protein accumulation within 1-2 weeks post infection with the
subsequent protein decreasing. In our case, the bright GFP fluorescence in
distal young leaves was visible even after 6 weeks post infection with PVX-
based genetic construction, suggesting that plants can be native reservoirs
for storage of proteins during a month before extraction. PVX-based vector
was chosen as a base for replacement gfp gene on col1A genes for collagen
production. Thus, we confirmed stable inheritance of target p4h gene in T1
progeny, showed that these plants are good hosts for recombinant protein
production, and chose a genetic construction suitable for further collagen
production.

57
YOUNG VS YOUNGER: bZIP TRANSCRIPTION FACTOR
NETWORKS AT TWO DEVELOPMENTAL STAGES

Liang Song, Milad Alizadeh

University of British Columbia, Botany, Vancouver, Canada

bZIP transcription factors (TF) play a pivotal role in plant stress responses
and development. Despite sharing conserved protein domains and binding
to similar cis-regulatory elements, ABA insensitive 5 (ABI5) and ABA-
responsive elements-binding factors (ABFs) exhibit both distinct and
overlapping functions. We generated the genome-wide binding profiles of
bZIP and other TFs. Thousands of TF target loci revealed the molecular
basis that defines the regulatory differences and similarities of these TF
networks. We will also discuss how these networks help to shape the
developmental stage-specific abiotic stress responses.

58
GENE REGULATORY NETWORKS AND CHROMATIN
REGULATION IN CONTROL OF SHOOT ARCHITECTURE

Jazmine Humphreys, Stephanie Kerr, Christopher Ray, Christine Beveridge,

Milos Tanurdzic

The University of Queensland, School of Biological Sciences, St Lucia,

Australia

Plant architecture is shaped by hormone signalling pathways regulating

gene expression resulting in a variety of plant forms and sizes. We have
explored early gene expression responses to a key shoot branching regulator
strigolactone (SL) and other plant hormones in Arabidopsis and garden pea
using a combination of transcriptomics, forward and reverse genetics,
chromatin accessibility profiling, and systems biology approaches. We
inferred gene regulatory networks based on gene co-expression, which we
further refined using experimental evidence. Our results show that hormone
signalling is partly convergent on the key branching regulator
BRANCHED1 (BRC1). We discovered direct genetic targets of BRC1 and
other transcriptional regulators using an inducible in vivo system and show
that the SL gene regulatory network consists of modules involving members
of Homeobox and TCP-domain transcription factors, as well chromatin
remodelling and post-transcriptional regulatory mechanisms relying on
transitive RNAi and alternative splicing. Our results also identify key
network nodes that allow for integration with other hormonal signals such
as cytokinins and abscisic acid, which, in concert, regulate shoot
architecture. We will also present results from a comparative analysis of SL
gene regulatory networks that identify conserved and derived GRN modules
and particular network components that highlight the points of divergence
in regulation of shoot branching between species.

59
GRAMENE KNOWLEDGEBASE: A UNIFYING RESOURCES FOR
COMPARATIVE GENOMICS AND PATHWAY ANALYSIS

Marcela K Tello-Ruiz1, Sharon Wei1, Andrew Olson1, Justin Preece2,

Sushma Naithani2, Parul Gupta2, Yinping Jiao1, Bo Wang1, Kapeel
Chougule1, Vivek Kumar1, Sunita Kumari1, Peter D'Eustachio3, Bruno
Contreras-Moreira4, Irene Papatheodorou4, Pankaj Jaiswal2, Doreen Ware1,5
1
Cold Spring Harbor Laboratory, Comparative Plant Genomics, Cold Spring
Harbor, NY, 2Oregon State University, Dept Botany & Plant Pathology,
Corvallis, OR, 3NYU School of Medicine, Dept Biochemistry & Molecular
Pharmacology, New York, NY, 4EMBL-European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, United Kingdom, 5USDA ARS
NEA, Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY

Gramene (http://www.gramene.org) is an integrated genomic and plant

pathway knowledgebase supporting the community of plant researchers,
breeders and educators in data exploration, visualization, and comparative
genomic analysis. With the availability of new genomes, gene annotations
and genetic diversity datasets, it is possible to assemble these datasets into a
single resource to semantically explore the nuances of speciation, ploidy,
adaptation, and effects of domestication and natural selection on the
genome structure, gene function, plant structure, phenotype, genome
evolution and adaptation. With this aim, the Gramene knowledgebase
provides a discovery environment with well-annotated genomic data sets
and tools to enable comparative functional analysis and formulate data-
driven hypotheses that can be tested experimentally. The knowledgebase
provides integrated search capabilities and interactive platforms to visualize
genome alignments, synteny, gene features, and gene neighborhoods for
about 2.3 million genes from 61 plant genomes, genetic diversity datasets in
the form of 224 million SNPs mapped to 12 reference genomes, over
93,000 phylogenetic trees with 1.9 million genes, gene expression profiles
from over 800 experiments and 24 species, genetic regulatory and metabolic
pathway networks, and connections to external resources. Gramene’s
pathway portal Plant Reactome hosts 298 reference pathways curated in rice
and projected to 82 additional plant species by orthology. Gramene is
committed to open access and FAIR data principles. We support data access
in various standardized formats as well as via web-based programming
interfaces (APIs). Extensive use of ontologies, database cross-references,
common data formats, metadata, community engagement and open-source
software promotes interoperability within the ecosystem of informatics data
and services. We will present use cases that are of interest to the plant
genomics and systems biology research community. Gramene is supported
by an NSF grant IOS-1127112, and partially from USDA-ARS (1907-
21000-030-00D).

60
CRISPR/CAS9 GENE EDITING OF SOYBEAN KAS1 ALTERS SEED
COMPOSITION TRAITS AND PLANT GROWTH

Kamaldeep S Virdi, Madison Spencer, Adrian O Stec, Ryan Merry, Aaron J

Lorenz, Robert M Stupar, Gary J Muehlbauer

University of Minnesota, Agronomy and Plant genetics, Saint Paul, MN

Seed composition traits are important targets in soybean improvement

programs. Previously, we reported a fast-neutron induced chromosome
translocation that disrupts 3-ketoacyl-acyl carrier protein synthase 1 (KAS1,
Glyma.08g084300) and provided genetic and biochemical evidence that
KAS1 may impact sucrose and oil concentrations. To validate our previous
results and conduct functional analysis, we employed CRISPR/Cas9 gene
editing to induce novel mutations in KAS1. Whole plant transformation
recovered various kas1 indel alleles in T0 plants, which were stably
inherited through the T2 generation. We used transformation event 677-3
carrying multiple mutations and generated five stable families carrying null
allele: 677-3-47(WT/WT), 677-3-35 (delta+107/delta+10), 677-3-44 (delta-
1/delta+1), 677-3-43 (WT/delta-1) and 677-3-48 (WT/delta+1). NIR scans
from greenhouse grown T3 seeds from these five families showed perfect
co-segregation of the mutations with high sucrose, high linolenic acid and
low oil phenotypes. On average, mutant segregants showed a remarkable
and statistically significant increase in sucrose, displaying 11.8% dry basis
in the mutants (wild type level was 6.0%). Linolenic acid also showed an
increase, jumping from 7.5% dry basis in the wild type to 17.0% in the
mutant. Meanwhile, total oil content decreased from 18.8% dry basis in the
wild type to 5.7% dry basis in the mutant. Interestingly, segregating
progeny from heterozygous parents showed non-Mendelian inheritance with
lower than expected transmission of mutant alleles. Seeds from T2 plants
carrying kas1 null alleles exhibited wrinkled and rough seed coat
phenotypes similar to the original fast neutron induced allele. Moreover, T3
kas1 plants also exhibited reduced plant height and slow growth. We
resequenced all of the edited lines at whole genome level. Preliminary PCR
based assay showed no off-targeting of guide-RNA for KAS1 paralog
(Glyma.05g129600). We have isolated one family 677-3-22-10 (WT/delta-
6) carrying an in-frame KAS1 allele. NIR data from progeny seed of
segragating T3 plants of this family will be presented. Our results
demonstrated that KAS1 is an important gene in oil biosynthesis and can be
utilized to alter both sucrose and oil composition traits in soybean.

61
VARIANT PHASING AND HAPLOTYPIC EXPRESSION FROM
SINGLE-MOLECULE LONG-READ SEQUENCING IN MAIZE

Bo Wang1, Elizabeth Tseng2, Primo Baybayan2, Kevin Eng2, Michael

Regulski1, Yinping Jiao1, Liya Wang1, Andrew Olson1, Kapeel Chougule1,
Peter Van Buren1, Doreen Ware1,3
1
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor,
NY, 2Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 3USDA
ARS, NEA Robert W. Holley Center for Agriculture and Health Cornell
University, Ithaca, NY

Haplotype phasing of genetic variants in maize is important for

interpretation of the genome, population genetic analysis, and functional
genomic analysis of allelic activity. Accordingly, accurate methods for
phasing full-length isoforms are essential for functional genomics studies.
We performed an isoform-level phasing study in maize, using two inbred
lines and their reciprocal crosses, based on single-molecule full-length
cDNA sequencing. To phase and analyze full-length transcripts between
hybrids and parents, we developed a tool called IsoPhase. Using this tool,
we validated the majority of SNPs called against matching short-read data
and identified cases of allele-specific, gene-level, and isoform-level
expression. Our results revealed that maize parental and hybrid lines exhibit
different splicing activities. After phasing 6,907 genes in two reciprocal
hybrids using embryo, endosperm and root tissues, we annotated the SNPs
and identified large-effect genes. In addition, based on single-molecule
sequencing, we identified parent-of-origin isoforms in maize hybrids,
distinct novel isoforms in maize parent and hybrid lines, and imprinted
genes from different tissues. Finally, we characterized variation in cis- and
trans-regulatory effects. Our study provides measures of haplotypic
expression that could increase accuracy in studies of allelic expression.

62
ACCESS TO MAIZECODE DATA VIA SCIAPPS.ORG

Liya Wang1, Zhenyuan Lu1, Xiaofei Wang1, Doreen Ware1,2

1
Cold Spring Harbor Laboratory, Plant Sciences, Cold Spring Harbor, NY,
2
USDA, ARS, Ithaca, NY

MaizeCODE, a project for an initial analysis of functional elements in the

maize genome, has assayed five tissues of four maize genomes (B73,
NC350, W22, TIL11) for RNA-seq, Chip-seq, Rampage, small RNA, and
MNase (outside collaboration). MaizeCODE is committed to open access
and reproducible science based on FAIR data principles, providing both
human and machine access to the data. There are three ways to access
MaizeCODE data: First, all raw data are available through CyVerse Data
Store, user can bulk download all data sets through iCommands (command
line) or CyberDuck (GUI); Second, all raw data and ground-level analysis
results of MaizeCODE data are available through SciApps
(https://www.SciApps.org), a cloud-based bioinformatics workflow
platform, for integrative analysis; Third, peaks and signals from ground
level analysis are available on JBrowser. In addition, all raw data has been
submitted to NCBI short read archive (SRA) using the SRA submission
pipeline in the CyVerse Discovery Environment (DE). Through the
submission process, all experimental metadata are stored in the iRODS
based Data Store of CyVerse and used for automating the ground level
analysis on SciApps. SciApps organizes both replicates (and controls if
available) of each assay as one experiment (or workflow with the unique
id), which represents an entity that chains raw data, analysis results,
experimental metadata, and computational metadata together. The ground
level analysis includes quality control (QC), alignment to the reference
genome, filtering, quantification (e.g. for gene expression), and peak calling
(if needed). SciApps provides both a Graphical User Interface (GUI) and a
RESTful API for users to check QC results, process new data, and
reproduce existing analysis on the Texas Advanced Computing Center
(TACC) cloud. MaizeCODE is supported by an NSF grant IOS 1445025;
SciApps is supported by an NSF grant DBI-1265383, and USDA-ARS
(1907-21000-030-00D).

63
GRAMENE SUBSITES: PANGENOME BROWSERS FOR CROPS

Sharon Wei1, Andrew Olson1, Marcela K Tello-Ruiz1, Joshua Stein1, Kapeel

Chougule1, Yinping Jiao1, Bo Wang1, Ivar Meijs1, Doreen Ware1,2
1
Cold Spring Harbor Laboratory, Ware Lab, Cold Spring Harbor, NY,
2
USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit,
Ithaca, NY

Continued advances in sequencing/assembly technologies are generating an

abundance of high quality reference assemblies within crop species,
ushering a transition from single-genome to pan-genome research
approaches. With this transition, communities will need ready access to pre-
computed comparisons of genome assemblies to identify and characterize
common and variable regions. To accommodate this need, the Gramene
comparative genomics project is developing Gramene subsites, each
dedicated to the study of individual crop groups. We will describe current
status on four pangenome subsites that support rice
(http://oge.gramene.org), maize (http://maize-pangenome-
ensembl.gramene.org), sorghum (https://www.sorghumbase.org) and
grapevine (http://vitis.gramene.org). A key feature of pan-genome subsites
is the application of uniform annotation protocols to minimize
methodological artifacts, and the application of Ensembl and Gramene
infrastructures for comparative analysis and visualization. Extending
Compara gene tree output, we define conserved syntelog sets and assign
conservation scores based on the proportion of genomes with membership
in each set. We then score individual genomes for presence/absence and
copy-number variation, additionally supported by whole genome
alignments. Using related approaches in the Oryza genus, we showed that,
compared to ancient families, recently emerged genes have higher rates of
evolution, higher lability, more limited expression, prevalence in
pericentromeric regions, reduced coding-length, and enrichment for stress-
response functions. We gratefully acknowledge support from grants
NSF#1744001, NSF#1127112, and USDA-ARS#58-8062-7-008.

64
VALIDATION OF GENETIC INTROGRESSION BY
INTERSUBGENERIC HYBRIDIZATION BETWEEN GLYCINE MAX
AND GLYCINE TOMENTELLA

Lucas B Santos2, Joao P Viana1, Wei Wei1, Xing Wu4, Anete P Souza2,
Matthew Hudson1, Steven J Clough3,1
1
University of Illinois, Crop Science, Urbana, IL, 2University of Campinas,
Plant Biology, Campinas, Brazil, 3US Department of Agriculture, Urbana,
IL, 4Yale University, Plant Molecular Biology, New haven, CT

Genetic bottlenecks impacted by soybean domestication and selective

breeding raise challenges for future soybean breeding programs to improve
yield or disease-resistance traits. Wild perennial Glycine species exhibit
vast genetic diversity that could be deployed to counteract the genetic
bottlenecks. Despite poor crossability, intersubgeneric hybridizations have
been made between cultivated soybean (Glycine max var. Dwight; 2n=40)
and Glycine tomentella (2n=78), a wild perennial relative of soybean (Singh
and Nelson 2015). However, although the derived progenies displayed
multiple morphological and disease resistance traits that resembled G.
tomentella, the genetic introgression from G. tomentella to G. max has yet
to be verified. Whole genome sequencing using the 10X Genomics
Chromium Technology was performed on 12ST4-5, a derived line from G.
tomentella x G. max, and Dwight, the recurrent G. max parent used in
crosses. Whole genome de novo assemblies were conducted using
Supernova v2 and yielded a scaffold N50 at 1.5Mb for 12ST4-5 and
206.32kb for Dwight. In order to search for potentially introgressed
sequences from G. tomentella, pairwise alignments between the two lines
were performed and 102 insertions larger than 1 kb were identified to be
present in 12ST4-5 but not Dwight. These putative introgressed sequences
were blasted against the Dwight and William 82 genomes, yielding 9 nine
sequences as potentially true presence/absence variants (PAVs). Six out of
the nine inserted sequences were further validated by PCR, increasing the
possibility of them originating from G. tomentella. Current results have yet
to verify introgression of large fragments, but have not ruled out transposon
activation or short sequence introgressions. To improve our ability to
determine if any of the unique regions in 12ST4-5 might have come from
G. tomentella, we are using additional sequencing platforms to try to build a
contiguous and unambiguous assembly of G. tomentella, including 10X
Genomics, Dovetail Genomics, Pacbio and Bionano.

65
NATURALLY OCCURRING VARIATION IN AN EPIGENETIC
CONTROL MECHANISM

Ben P Williams, Drew Cohen, Mary Gehring

Whitehead Institute for Biomedical Research, MIT, Cambridge, MA

Epigenetic information such as DNA methylation is stably inherited over

multiple cell divisions and reproductive generations. How the enzymes that
add and remove DNA methylation are coordinated to ensure this stability
remains unclear. The gene encoding the primary somatic DNA demethylase
ROS1 is activated by DNA methylation at its transcriptional start site,
which ensures homeostasis between methylation and demethylation
pathways. Analysis of hundreds of naturally occurring Arabidopsis strains
identified an ecotype, Cerv-1, naturally defective in ROS1 methylation.
Cerv-1 ROS1 expression is 100-fold lower than other ecotypes and is
uncoupled from its DNA methylation state. Recombinant hybrids between
Cerv-1 and Col-0 will provide an excellent opportunity to identify trans-
acting factors underpinning the unusual and enigmatic regulation of ROS1.

66
INSECT HERBIVORY ELICITS FLOWER DEVELOPMENT GENE
NETWORKS AS INDUCED DEFENSE IN TOMATO LEAVES

Lanlan Ke*1, Yangzi Wang*2, Thomas Städler3, Yuanyuan Song4, Renseng

Zeng1,4, Shuqing Xu2
1
Fujian Agriculture and Forestry University, College of Life Science,
Fuzhou, China, 2University of Münster, Institute for Evolution and
Biodiversity, Münster, Germany, 3ETH Zürich, Department of
Environmental Systems Science, Zürich, Switzerland, 4Fujian Agriculture
and Forestry University, College of Crop Science, Fuzhou, China

Herbivory-induced defenses are widespread, rapidly evolving and relevant

for plant fitness. Such induced defenses often involve transient
accumulations of jasmonic acid (JA), reconfigurations of metabolisms, and
release of volatiles in leaves, the processes of which are also found during
flower development. Furthermore, recent functional studies showed that
several key genes and metabolites in induced defenses are also associated
with flower development. Therefore, we hypothesized that herbivory elicits
flower development gene networks in leaves, which were recruited for
induced defenses. To test this hypothesis, we sequenced 216 transcriptomes
of flowers at different developmental stages and tobacco hornworm
(Manduca sexta) feeding-induced leaves in seven closely related tomato
species. Using gene co-expression network analysis, we identified key gene
modules involved in herbivory-induced defenses and flower development,
respectively. Comparative analysis revealed that a significantly large
number of gene regulatory networks were shared between herbivory-
induced defenses and flower development. Analyzing patterns of expression
divergence within and between species further showed that herbivory-
induced defenses in leaves co-evolved with flower development in tomato.
Together, this study provided evidence that herbivory-induced defenses
recruited flower development gene networks in tomato. The intrinsically
shared regulatory networks between the two seemingly distinct biological
processes might result in co-evolution of plant defenses and floral signals in
plants.

*: these authors contributed equally.

67
MOLECULAR CHARACTERIZATION OF ARABINOXYLAN FIBERS
IN OAT

Jose A Zambrano, Olof Olsson

Lund University, Pure and Applied Biochemistry, Lund, Sweden

Oat (Avena sativa) is a very valuable crop for Swedish agriculture and food
industry. It is cultivated both for its positive agricultural characteristics and
great nutritional value. Oat is currently ranked seventh in total world cereal
production. Oat contains a number of unique bioactive compounds like
antioxidants, inositol phosphates, fibers, starches, vitamins, galactolipids
and the highest levels of globular proteins amongst any cereal. All these
properties have health beneficial effects on both humans and animals.

In the last 15 years, our research group has been working on the
development of new oat varieties with specific properties. Using a
mutagenized oat population, we have identified lines with high β-glucan,
protein, lipid and avenathramide contents in the kernels as well as lines low
in seed coat lignin content. Recently we initiated research on arabinoxylan
fibers, due their function as main components of soluble and insoluble
dietary fibers. However, the specific role of arabinoxylan fibres is not clear
at present, neither when it comes to active levels or required structural
properties. The function of arabinoxylan in other crops such as barley or
wheat is well known but nevertheless, the information available is scarce
when it comes to oats.

Our goal is to understand both the biosynthesis and regulation of

arabinoxylans in oats, their biological role in oat and their health effects in
humans. As a first step, we aim to develop new oat lines with high
arabinoxylan content. Using a special chromatography techniques
(HPAEC), we have successfully developed a quantitative arabinoxylan
assay for cereals. Using this assay, we have compared arabinoxylan
contents between different cereals as well as between different lines from
our mutagenized population.

The next part of the project will focus on the characterization of structures
of arabinoxylan fibres in mutated lines with especially high arabinoxylan
levels. From the oat genome, which we have sequenced, we will also
identify all sequencences associated with arabinoxylan and elucidate
molecular mechanisms behind arabinoxylan biosynthesis.

68
HIGH-RESOLUTION EXPRESSION QUANTITATIVE TRAIT
NUCLEOTIDE (eQTN) MAPPING ELUCIDATES TRANSCRIPTIONAL
REGULATION IN POPULUS TRICHOCARPA

Jin Zhang1, Jeremy Schmutz2, Gerald Tuskan1, Wellington Muchero1, Jin-

Gui Chen1
1
Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN,
2
HudsonAlpha Institute for Biotechnology, Huntsville, AL

Genetic control of transcriptional regulation is highly complex in higher

plants, especially in woody species. To reveal the genetic regulatory
landscape in the woody model plant Populus trichocarpa, we performed an
expression quantitative trait nucleotide (eQTN) mapping enabled by the
whole-genome resequencing and RNA-seq analysis of gene expression. A
panel of > 8.2 million single nucleotide polymorphisms (SNPs) and
nucleotide insertions and deletions (InDels) were obtained from whole-
genome resequencing of 917 unrelated individuals of P. trichocarpa. From
390 leaf and 444 xylem transcriptome data, 16,030 and 15,496 genes,
respectively, exhibited significant expression variation across the
population. After integrative analysis, cis- and trans-eQTNs were identified
controlling gene expression in both tissues. Enriched transcription factor
binding sites (TFBS) including cis-eQTN showed tissue-specific
divergence. trans-eQTN analysis identified multiple hotspots that were
significantly associated with expression of more than 100 putative target
genes. In addition, genome-wide association studies (GWAS) of multiple
phenotypes including drought-induced leaf senescence, stem canker and
leaf spot caused by the fungal pathogen Sphaerulina musiva, and
metabolome profiling revealed key genes that are highly associated with
those phenotypes. Combined with the eQTN mapping, the upstream
regulators of these phenotype-associated genes and their regulatory network
were identified providing an understanding of the complex regulatory
mechanisms underlying trait expression. For instance, we have successfully
identified mutations in a cis-element controlling expression of a cation/H+
antiporter that regulates poplar leaf senescence under drought stress. The
eQTN study provides powerful tools for identifying transcriptional
regulators underlying complex phenotypes of woody species.

69
CHARACTERIZING KEY REGULATORS OF PRIMARY ROOT
DEVELOPMENT

Lifang Zhang1, Andrew Olson1, Fangle Hu1, Allison Gaudinier2, Siobhan

Brady2, Doreen Ware1,3
1
Cold Spring Harbor Laboratory, Ware, Cold Spring Harbor, NY, 2UC
Davis, Plant Biology & Genome Center, Davis, CA, 3USDA-ARS-NAA,
Ithaca, NY

Roots are essential plant organs that provide structural support and are
primarily responsible for acquisition of water and certain mineral nutrients.
To improve our understanding of the genes controlling root development,
we are using a gene centered approach to characterize upstream regulators
of miRNAs known to be involved in root development. Our approach uses a
nearly complete root transcription factor (TF) library to screen promoters of
root development related miRNAs and their targets. The result is a
regulatory network of protein-DNA interactions, between transcription
factors and the promoters of miRNAs and their down-stream targets. We
have combined this with known and predicted miRNA targets and publicly
available genome wide protein-DNA interaction data, thus forming a more
complete Gene Regulatory Network (GRN). We further utilize extensive
high resolution spatial and temporal gene expression data, and use models
to infer significant interactions and predict key regulators of root
development. This information was used to prioritize a set of genetically
perturbed lines for evaluating their root developmental phenotype.

70
MAINTENANCE OF HETEROCHROMATIN CAUSES NATURAL
EPIGENETIC VARIATION IN ARABIDOPSIS THALIANA

Yinwen Zhang1, Jered M Wendte2, Lexiang Ji1, Bob Schmitz2

1
Institute of Bioinformatics, University of Georgia, Athens, GA,
2
Department of Genetics, University of Georgia, Athens, GA

In plants and mammals, DNA methylation functions in maintaining genome

stability by silencing transposable elements in the heterochromatin, and in
regulating development by affecting the expression of a subset of genes in
the euchromatin. We have previously shown that genome-wide methylation
patterns in Arabidopsis thaliana are highly stable over generational time
scales, with the exception of rare epialleles. However, such an apparent
stability appears to be maintained dynamically and involves the interactions
between euchromatin and heterochromatin. Here we describe the finding
that both heterochromatin DNA methylation and genic DNA methylation
are highly variable among 725 Arabidopsis thaliana accessions, thus
providing an excellent opportunity to understand the source, mechanistic
basis, specificity and consequence of variations in genic methylation over
an evolutionary time scale. We found that the amount of genic DNA
methylation is inversely correlated with that in heterochromatin, suggesting
that certain methylation pathway(s) may be redirected to target genes upon
the loss of heterochromatin. This redistribution likely involves a feedback
loop involving the DNA methyltransferase, CHROMOMETHYLASE 3,
H3K9me2 and histone turnover, as long genes with a high density of CWG
sites and which are expressed are more likely to be targeted. Importantly,
although the presence of CG methylation in genes alone may not affect
transcription levels, genes containing CG methylation are far more likely to
become subsequently methylated at non-CG sites and transcriptionally
silenced as seen in transposable elements. Taken together, these results
underscore the importance of a balance between heterochromatin and
euchromatin, and unveiled a major potential factor underlying the
emergence of epialleles during evolution.

71
BUILDING A COMPUTATIONAL FRAMEWORK OF CELL TYPE-
SPECIFIC C4 PLANT MULTISCALE MODELING TO ENHANCE
BIOMASS PRODUCTION UNDER DROUGHT IN SORGHUM

Cheng Zhao1, Pascal Schläpfer1, Edward J Wolfrum2, Jennifer Barrett3,

Allen Hubbard3, Hui Jiang3, Xiaoping Li3, Erica Agnew3, Todd Mockler3,
Ivan Baxter3, Sue Rhee1
1
Carnegie Institution for Science, Department of Plant Biology, Stanford,
CA, 2National Renewable Energy Lab, Golden, CO, 3Donald Danforth Plant
Science Center, St. Louis, MO

C4 plants, such as Sorghum, have CO2 concentrating mechanism in

specialized cell types (bundle sheath and mesophyll cells) to enhance water
use and photosynthetic efficiencies. Mathematical modeling of C4
photosynthesis does not sufficiently capture leaf biochemical and
anatomical phenotypes under dynamic environments. In this study, we
present a computational framework of multiscale modeling to investigate
how plants allocate metabolic resources for biomass production in response
to drought. The framework is centered on a cell type-specific genome-scale
metabolic network model of S. bicolor, generated from a generic Sorghum
model constrained by cell type-specific RNA-seq data. A C4 photosynthesis
biochemical model was then integrated with the cell type-specific model to
simulate dynamic environments by controlling carbon and energy sources
of the metabolic network model. We collected a variety of data to inform
the metabolic network model, such as photosynthesis data, biomass
composition data and RNA-seq data for Sorghum under well-watered and
water-limiting conditions at multiple time points. To identify the key
reactions that limit biomass production under drought conditions, we are
currently performing Flux Variability Analysis to determine the maximum
range of flux that every reaction can possibly take while the network is
optimized for biomass production. Predictions will be tested by performing
metabolomics experiments of knock-out lines of candidate genes under
drought.

72
DELINEATING TISSUE- AND CONDITION- SPECIFIC
TRANSCRIPTIONAL REGULATION OF METABOLISM IN
ARABIDOPSIS THALIANA

Kangmei Zhao1, Michael Banf1,2, Pascal Schläpfer1,3, Sue Rhee1

1
Carnegie Institution for Science, Department of Plant Biology, Palo Alto,
CA, 2Max Planck Institute, Plant Breeding Research, Cologne, Germany,
3
ETH Zürich, Department of Biology, Zürich, Swaziland

Coordinated control of metabolic genes plays an important role for plant

development and adaptation to various environments, but we still lack the
systematic understanding of transcriptional regulation of metabolic genes
and pathways. Here, we sought to discover general rules of metabolism
regulation in Arabidopsis thaliana by integrating omics data, ensemble
modeling, and experimental validation. We aimed to understand how
transcription factors regulate metabolism by developing a novel algorithm
called MERIT and constructing a condition- and tissue-specific regulatory
network. Experimentally characterized interactions between transcription
factors and target genes showed that our network outperformed existing
regulatory networks in Arabidopsis. We systematically identified 31
transcription factor families that play predominant roles in regulating
metabolism. Moreover, we identified master regulators that control the
majority of genes involved in each metabolic domain and these master
regulators indicate less tissue- and condition-specificity. At a single
pathway level, most transcription factors directly controlled only a small
fraction (< 25%) of the genes involved in a pathway. We predicted novel
regulators associated with 85% of total pathways in Arabidopsis. Using
phenylpropanoid biosynthesis pathway as an example, we are testing the
ability of novel putative regulators on altering the biosynthesis of the
metabolites. This study expands our current understanding of metabolism
regulation and contributes to developing toolkits for pathway engineering in
plants.

73
QUANTITATIVE AND GENOME-WIDE ANALYSIS OF A
TRANSCRIPTION FACTOR MODULE INTEGRATING LIGHT- AND
HORMONE-SIGNALING PATHWAYS IN ARABIDOPSIS

Jia-Ying Zhu, Zhi-Yong Wang

Carnegie Institution for Science, Department of Plant Biology, Stanford,

CA

Plants respond to both internal and external signals by integrating these

signals through structured intercellular networks. Our previous studies have
shown that phytohormone brassinosteroid and auxin signal transduction
pathways are integrated with light and temperature. This integration occurs
through a transcription factor module. This module consists of three
transcription factors: BRASSINAZOLE-RESISTANT 1 (BZR1), AUXIN
RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING
FACTOR 4 (PIF4). Using ChIP-Seq, we showed that these transcription
factors bind to overlapping sets of target genes to control cell elongation
and photomorphogenesis, which explains conceptually how diverse signals
are integrated into coherent cell growth decisions. While ChIP-seq binding
profiles show direct binding of transcription factors and multiprotein
complexes under complex cellular conditions, how cis-regulatory element
combinations and interacting transcription factors define the overlapping
target gene sets and fine-tune transcription factor activities remain to be
answered. Here, we analyze transcription factors-genome binding affinity in
vitro by quantitative measurement of binding affinities of BZR1, ARF6, and
PIF4 complex to the genomic cis-regulatory elements under defined
conditions without interference of chromatin and unknown factors.
Furthermore, by labeling transcription factors with different fluorescent
substrates, both equilibrium binding constants and dissociation kinetics can
be determined for a transcription factor at each of the millions of genomic
DNA fragments, and the binding of pairwise or multiple transcription
factors can be measured simultaneously to detect cooperation or
competition between transcription factors at each DNA fragment. Such
analysis can reveal how combinatorial interactions between transcription
factors and transcription factor-DNA refine target selectivity and allow
transcriptional crosstalk.

74
A PLANT SECONDARY METABOLITE MODIFIES BACTERIAL
TRANSCRIPTION FACTOR TO INHIBIT VIRULENCE

Jian-Min Zhou

State Key Laboratory of Plant Genomics, Institute of Genetics and

Developmental Biology, Chinese Academy of Sciences, none, Beijing,
China

Different from commensal microbes, phytopathogenic microbes deploy

specialized weapons to defeat host defenses. Pseudomonas syringae uses
the type III secretion system to inject effectors into the plant cell to subvert
host immunity and is essential for pathogenesis. A great deal is known
about mechanisms by which plants perceive microbial signals to activate
immune responses. Much less is known how plant secondary metabolites
halt pathogen aggression. We set out to test the hypothesis that at least some
plant secondary metabolites are capable of inhibiting P. syringae type III
system. Indeed, we found that Arabidopsis extracts are highly potent in the
inhibition of P. syringae type III system. Through purification, structural
elucidation, and chemical synthesis, we demonstrate that sulforaphane
(SFN), a derivative of aliphatic glucosinolate, is capable of inhibiting P.
syeingae type III gene transcription. Although the apoplast, where the
pathogen resides, only possesses ~20 μM SFN in undamaged tissues, this
concentration is sufficient to inhibit P. syringae type III gene expression
both in vitro and in planta. Plants defective in SFN production is unable to
attenuate bacterial virulence and display increased susceptibility to P.
syringae. Furthermore, SFN target profiling, in situ modification, and
mutagenesis analyses demonstrated that SFN attenuates bacterial virulence
by modifying Cys209 of HrpS, a key transcription factor controlling type III
gene expression in P. syringae. Interestingly, Arabidopsis SFN does not
affect leaf-associated bacterial microbiota, suggesting that SFN in healthy
tissues does not impact beneficial microbes.

75
LOTUS JAPONICUS AND RHIZOBIA INTERACTIONS; FROM
SIMPLE TO COMPLEX ASSOCIATIONS

Simona Radutoiu

Aarhus University, Department of Molecular Biology and Genetics, Aarhus,

Denmark

Legume-rhizobia interactions are controlled by protein-carbohydrate

recognition events that take place at the epidermal-soil interface. Legumes
use LysM proteins to recognize carbohydrates produced by pathogens or
symbionts. This suggests that an ancient recognition process has been used
in legumes for evolution of elaborated mechanisms for various carbohydrate
perceptions.

In Lotus japonicas two LysM receptor kinases, NFR1 and NFR5, initiate
root nodule symbiosis after perception of Nod-factors secreted by M. loti,
while EPR3 scrutinizes rhizobial exopolysaccharides controlling the
elongation of infection threads. Lotus encodes several additional LysM
receptors, and we have used reverse genetics coupled with in planta
functional studies to study their role in Lotus. Our studies based on binary
interactions identified novel components involved in carbohydrate signaling
that contribute to the ability of Lotus to distinguish symbiotic and
pathogenic microbes.

Recent analyses of bacterial taxa associated with roots of soil-grown Lotus

wild-type and symbiotic mutant plants identified a previously unsuspected
role of the nodulation pathway in the establishment of distinctive bacterial
assemblages in root and rhizosphere. However, the role of soil microbiota
on legume-Rhizobium symbiosis is currently unknown. We have employed
specific members of a newly established culture collection to investigate the
complex Lotus-Rhizobium-soil bacteria interactions in tailored microcosms.
Our findings from these investigations based on plant and bacterial mutants
will be presented.

76
SYNTHESIS OF INDOLE-3 ACETIC ACID BY APHID SALIVA

Leila Feiz, Navid Movahed, Georg Jander

Boyce Thompson Institute, Cornell University, Ithaca, NY

Aphids have evolved specialized saliva that they inject into phloem sieve
elements to ensure a successful interaction with their host plants. A variety
of proteins and small molecules, most of which are either completely
unknown or their functions remain to be determined, have been identified in
aphid saliva. To investigate the composition of the aphid saliva, we used
high-resolution mass spectrometry to analyze aphid-fed artificial diet. One
metabolite that we detected is indole-3-acetic acid (IAA), a phytohormone
that is well known for its role in regulating plant growth and development.
By means of stable isotope labeling, we determined that the accumulation
of IAA in aphid diet requires aphid feeding, and that this biosynthesis is
both tryptophan-dependent and enzymatic. Further experiments showed that
aphid feeding leads to accumulation of two inactive, oxidized catabolites of
IAA, oxindole-3-acetic acid and 5-hydoxy indole-3-acetic acid, in host
plants. This observation suggests that, to prevent metabolic manipulation by
aphids, plants may inactivate the aphid-derived auxin by oxidizing it.

77
FUNCTIONAL GENOMICS OF RHIZOSPHERE-ASSOCIATED
PSEUDOMONAS

Cara H Haney

The University of British Columbia, Microbiology & Immunology,

Vancouver, Canada

Plant root-associated microbial communities (the “rhizosphere

microbiome”) influence plant growth and defense. Closely-related bacteria
can have dramatically different effects on plant health and range from
pathogenic to mutualistic. As a result, the function of a community cannot
be predicted by taxonomic (e.g. 16S rRNA sequencing) methods alone.
Using beneficial Pseudomonas spp. and Arabidopsis as a tractable
rhizosphere microbiome model, we are using a combination of comparative
genomics and functional assays to correlate microbiome function with the
presence of certain genes in the plant microbiome. Using these approaches,
we have identified the genetic basis of 1) Pseudomonas modulation of plant
immunity and 2) Pseudomonas opportunistic pathogenesis. Collectively,
this work will inform our understanding of the genetic and molecular basis
of plant microbiome effects on plant health.

78
RESISTANCE-RELATED DIVERSITY IN CEREALS RESPONSE TO
PATHOGEN INFECTION.

Anna Piasecka1,2, Aneta Sawikowska2,3, Natalia Witaszak1, Agnieszka

Waśkiewicz4, Joanna Kaczmarek1
1
Institute of Plant Genetic of the Polish Academy of Sciences, Poznan, Poland,
Metabolomic Team, Poznan, Poland, 2Institute of Bioorganic Chemistry of the
Polish Academy of Sciences, Department of Plant Functional Metabolomic,
Poznan, Poland, 3Poznan University of Life Sciences, Department of
Mathematical and Statistical Methods, Poznan, Poland, 4Poznan University of
Life Sciences, Faculty of Wood Technology, Poznan, Poland

Fusarium head blight (FHB) is dangerous fungal disease of crop plants due to
substantial yield reduction and production of mycotoxins in the infected grains.
The creation of crops cultivars resistant to FHB is becoming increasingly
important for plant breeding. The breeding progress is not possible without a
thorough examination of the molecular basis of plant responses to biotic stress,
such as FHB. However, the immune mechanisms of cereals are until now
poorly known. Therefore, comprehensive and integrated research, in particular
in field of metabolomics, proteomics and transcriptomics were applied for
fundamental knowledge on plant immunity in cereal crops.
Studying differences in response to FHB between resistant and susceptible
cultivars of barley (Hordeum vulgare) and wheat (Triticum aestivum L.), as
well as closely related to them and well genetically characterized purple false
brome (Brachypodium distachyon) we were able to explore the resistance-
related metabolites and proteins in species from Poaceae family. We also
examined level of grain infection by fungal pathogen and mycotoxins
accumulation. In susceptible wheat cultivar there was more than 10 times higher
accumulation of zearalenon, one of the most dangerous mycotoxin, than in
resistant cultivar. For barley resistance-related differences were not so
significant. The same trend was observed for fungal infection which indicated
on efficient mechanism for preventing fungal penetration in resistant cultivars
of wheat. Interestingly, metabolomics and proteomic changes were strongly
diversified between resistant and susceptible cultivars. For one of the
differentially accumulated, tryptophan – derived metabolite, serotonin, the
accumulation was high in susceptible cultivars both in wheat and barley
whereas in resistant counterparts the accumulation was low. Opposite effect was
observed for hydroxycinnamic acid polyamines feruloylserotonin and p-
coumaroylserotonin. These results indicate a tight correlation of tryptophan and
hydroxycinnamic acid metabolism with cereals resistance to fungal pathogens.
Studies on common elements for cereals defense mechanisms will in future
facilitate the breeding of cultivars with improved resistance to fungal pathogens.
Statistical analyses for the experiments with multifactorial structure were
performed using our own scripts and procedures in Genstat. Visualizations were
performed in R.

This study was supported by the National Science Centre grants: Sonata
2015/17/D/NZ9/03347

79
FUNCTIONALLY ANTAGONISTIC INTEGRATED DOMAINS OF
THE RPG5 NLR IMMUNITY RECEPTOR INTERACT TO REGULATE
STEM RUST RESISTANCE IN BARLEY

Shyam Solanki1,2, Gazala Ameen1,2, Deepika Arora2, Pawel P Borowicz3,

Robert S Brueggeman1,2
1
Washington State University, Department of Crop and Soil Sciences,
Pullman, WA, 2NDSU, Plant Pathology, Fargo, ND, 3NDSU, Animal
Sciences, Fargo, ND

The integrated decoy hypothesis describes nucleotide binding leucine rich

repeat (NLR) resistance gene loci with two head-to-head NLRs. One NLR
contains an integrated domain (ID) that represents a host virulence effector
target that was duplicated and translocated to the NLR as pathogen “bait”.
The barley NLRs, Rpg5 and HvRga1, are required for resistance to Puccinia
graminis f. sp. tritici (Pgt), the wheat stem rust pathogen, and have the
head-to-head architecture of an ID locus. The majority of susceptible lines
contain a protein phosphatase 2C (rpg5-PP2C alleles) ID that compromise
resistance provided by the functional Rpg5 alleles that contain a serine
threonine kinase (STPK) ID in a dominant manner explaining RMRL-
mediated recessive resistance. The interaction of the antagonistic and allelic
IDs suggests retained biological function post integration, thus do not
represent integrated decoys. Confocal microscopy showed Pgt host entry
through stomata in the dark expelling the current dogma that a light period
is required for guard cell opening and pathogen entry, suggesting stomatal
manipulation by Pgt. The Rpg5 STPK ID progenitor, PRK1, an Arabidopsis
guard cell kinase AtAPK1b ortholog, is nearly identical to the Rpg5 STPK
but located at a distinct locus. A Y2H screen with Rpg5 STPK and PP2C
domains as bait identified the HvVOZ1 as an interactor. In Arabidopsis a
voz1voz2 mutant had reduced stomatal opening during drought stress.
RNAscope RNA in situ visualization identified low AtAPk1b expression
specific to guard cells in Arabidopsis. Similarly, PRK1 in barley showed a
low expression in guard cells suggesting it may still have the conserved
guard cell function. However, PRK1 and Rpg5-STPK were also found to be
expressed in the mesophyll cells suggesting the evolution of expression may
have facilitated the use of the proteins to bait haustorial expressed effectors
that interact with these STPK proteins. We are utilizing laser micro-
dissected leaf tissue RNAseq library to identify genetic components
operating during the early stomatal manipulation event in barley-Pgt
interaction. We posit that the stomatal closure at night in barley triggered
the evolution of Pgt effectors that act on PRK1 to trick the stomates to open
for incognito host entry. This pathogen manipulation of PRK1 forced the
host to evolve the Rpg5-STPK NLR-ID which recognizes the pathogen’s
attempt to manipulate PRK1 leading to the activation of defense responses;
a new paradigm in the barley-stem rust interactions.

80
IMPROVING PHOTOSYNTHETIC EFFICIENCY FOR IMPROVED
CROP YIELD

Paul F South, Amanda P Cavanagh, Donald R Ort

University of Illinois, Institute for Genomic Biology, Urbana, IL

Feeding the world’s current population already requires 15% of the total net
primary productivity of the globe’s land area and that will need to increase
to 25% in order to meet the projected increase in agricultural demand this
century. This near doubling of food production will have to be
accomplished on globally declining acreage and during a time in which
there will be ever increasing demand on cultivated lands for the production
of bioenergy crops, while in the face of a changing global environment that
has already resulted in decreasing global yield of some of the world’s most
important food crops. The yield potential of crops is determined by their
efficiency of capturing available light energy (Σi), the efficiency of
converting intercepted light into biomass (Σc), and the proportion of
biomass partitioned into grain (η). The remarkable yield gains of the Green
Revolution in the middle of the 20th century resulted from plant breeders
bringing η and Σi for major crops close to their theoretical maxima, leaving
improved photosynthetic efficiency as the only yield potential determinant
with sufficient capacity to double crop productivity. Opportunities to
improve photosynthetic efficiency exist in readapting photosynthesis to the
rapid changes in atmospheric composition and temperature, in redesigning
photosynthesis for agricultural production and in applying synthetic biology
to bypass evolutionary limitations and inefficiencies in photosynthesis.
Recent work using a synthetic biology approach to lower the energetic cost
of photorespiration will be presented.

81
DISCOVERY AND ENGINEERING OF PLANT CHEMISTRY FOR
PLANT AND HUMAN HEALTH

Elizabeth Sattely

Stanford University and HHMI, Stanford, CA

Plants are some of the best chemists on the planet and produce an
impressive array of small molecules. We are inspired by the fact that
humans have become extraordinarily reliant on plant-derived molecules for
food, medicine, and energy. However, remarkably little is known about how
plants make these molecules, limiting our ability to engineer and optimize
plant metabolic pathways. New plant genome sequences and synthetic
biology tools have enabled three research areas under investigation in my
lab: 1) Identifying the minimum set of enzymes required to make known
plant-derived molecules and non-natural derivatives through metabolic
engineering, and 2) discovering new molecules from plants, and 3)
developing new strategies to enhance plant fitness. In this talk, I will
describe some of our recent efforts to accelerate the discovery of complete
plant pathways for known and novel molecules, not only in the model plant
Arabidopsis but also in non-model plants.

82
IDENTIFICATION AND CHARACTERIZATION OF NOVEL
REGULATORS OF LOW-ENERGY-SIGNALING BY SnRK1 IN
ARABIDOPSIS THALIANA

Jennifer Bortlik1, Frederik Börnke1,2

1
Leibniz-Institute Grossbeeren, Plant Metabolism, Grossbeeren, Germany,
2
University of Potsdam, Plant Metabolism, Potsdam, Germany

In plants, the Sucrose non-fermenting (SNF1)–related protein kinase 1

(SnRK1) represents a central integrator of low energy signaling and
acclimation of towards many environmental stress responses. Although
SnRK1 acts as a convergent point for many different environmental and
metabolic signals to control growth and development, it is currently
unknown how this array of different signals could be translated into a cell-
type or stimulus specific response since many components of SnRK1-
regulated signaling pathways remain unidentified. Recently, we have
demonstrated that proteins containing a domain of unknown function (DUF)
581 interact with the catalytic alpha subunits of SnRK1 (AKIN10/ 11) from
Arabidopsis thaliana and could potentially act as mediators conferring
tissue- and stimulus-type specific differences in SnRK1 regulation. In order
to investigate how DUF581 protein function is related to SnRK1 signaling,
we systematically screened for phenotypic changes in DUF581 knock-out
and overexpression plants. We show here that modulation of DUF581
expression affects plant growth in an isoform dependent manner. While
plants overexpressing DUF-19 are smaller than the wild type, DUF9
overexpression plants show accelerated growth and biomass accumulation.
Biochemical evidence suggests that DUF9 acts as negative regulator of
SnRK1 activity by inhibiting SnRK1 T-loop phosphorylation through
upstream kinases. Transcriptional profiling of plants with altered DUF9
expression revealed differential expression of genes related to nitrate
assimilation, providing a possible explanation of increased growth in DUF9
overexpression plants. In summary, we provide evidence that DUF581
domain proteins can affect SnRK1 activity in an isoform specific manner to
link energy signaling to different cellular signaling and metabolic pathways
to integrate different environmental stimuli.

83
BIOSYNTHESIS OF CARDIAC GLYCOSIDES IN WALLFLOWERS
(ERYSIMUM, BRASSICACEAE)

Tobias Züst1, Susan R Stickler2, Adrian F Powell2, Mackenzie E Mabry3,

Hong An3, Mahdieh Mirzaei1, Thomas York2, Cynthia K Holland2, Pavan
Kumar2, Matthias Erb1, Georg Petschenka4, José María Goméz5, Francisco
Perfectti6, Caroline Müller7, Chris Pires3, Lukas A Mueller2, Georg Jander2
1
University of Bern, Institute of Plant Sciences, Bern, Switzerland, 2Boyce
Thompson Institute, Ithaca, NY, 3University of Missouri, Division of
Biological Sciences, Columbia, MO, 4Justus-Liebig-Universität Giessen,
Institut für Insektenbiotechnologie, Giessen, Germany, 5Estación
Experimental de Zonas Áridas, Department of Functional and Evolutionary
Ecology, Almería, Spain, 6University of Granada, Department of Genetics,
Granada, Spain, 7Bielefeld University, Department of Chemical Ecology,
Bielefeld, Germany

Accumulation of cardiac glycosides, small molecule inhibitors of animal

Na+/K+ ATPases, evolved independently as a defensive trait in at least
twelve plant families. However, despite the medically relevant properties of
cardiac glycosides, the complete biosynthesis pathway has not been
identified in any plant species. Within the Brassicaceae, the Erysimum
genus is unique in its accumulation cardiac glycosides. To provide insight
into cardiac glycoside biosynthesis, we sequenced the genome of Erysimum
cheiranthoides (wormseed wallflower) and the foliar transcriptomes of 47
additional Erysimum species. Metabolite profiling identified almost 100
different cardiac glycosides, with up to fifty in some individual Erysimum
species. Comparison of the cardiac glycoside content and a transcriptome-
based Erysimum phylogeny provided evidence for rapid gain and loss of
enzyme functions. There appears to be no tradeoff between the production
of glucosinolates, characteristic defensive metabolites of plants in the
Brassicaceae, and cardiac glycosides in Erysimum. We found candidate
genes for cardiac glycoside biosynthesis in E. cheiranthoides with a
combination of ethylmethanesulfonate mutagenesis, co-expression analysis,
and genetic mapping of natural variation in cardiac glycoside content.
Enzymatic functions of the identified genes were tested with
Agrobacterium-mediated transient expression and virus-induced gene
silencing.

84
RECONSTRUCTING PLANT METABOLISM WITH SYNTHETIC
BIOLOGY

Patrick M Shih

University of California, Davis, Davis, CA

There is great promise in using plants as chassis for a number of

biotechnological applications; however, the tools and approaches needed for
such endeavors are still in their infancy. We have developed various
synthetic biology tools to facilitate complex metabolic engineering in
plants. Specifically, we have used these approaches to optimize the
production of target bioproducts and commodity chemicals.

85
UNDERSTANDING CELLULAR METABOLISM USING SYSTEMS
ENGINEERING APPROACHES

Jin Wang

Auburn University, Chemical Engineering, Auburn, AL

Biological systems and large-scale industrial processes share many

similarities at the systems level: they both consist of many individual
components; they both have built-in feedback control/regulation
mechanisms; and the properties of the overall systems are determined by the
complex interaction among different components. Their complex natures
make the integrative systems approaches essential in understanding,
controlling and optimizing these systems. As a result, many process systems
engineering principles and techniques have been extended into the emerging
field of systems biology. In addition to their commonalities at the systems
level, however, biological systems have their own unique characteristics
and challenges. Existing systems engineering tools, developed for
engineered systems, cannot fully address these challenges.

In this talk, our most recent progress made in developing systems

engineering approaches for biological systems are presented. One specific
research goal is to effectively utilize genome-scale metabolic models
(GEM) to aid the understanding of complex cellular metabolism, i.e., how
to extract biologically meaningful information from numerical solutions
generated by GEMs. The solution we developed is a systems identification
based framework for GEM analysis. This framework enables the extraction
of the knowledge embedded in the GEM and visualization of the extracted
knowledge in a way that is easily accessible to people without background
in GEM. In this talk, we will use a xylose fermenting yeast,
Scheffersomyces stipitis, as the model system to illustrate the developed
framework. In addition, from a control perspective, dynamic response
during the transition between two steady states could offer key information
on the regulatory mechanism of the system. However, measuring and
analyzing dynamic responses is highly challenging for biological systems.
In this talk, we will examine the transition of S. stipitis from aerobic growth
to oxygen-limited fermentation with transcriptomic profiling. In this case
study, we highlight the importance of examining system’s dynamic
response, and how GEM can be integrated with machine learning to
discover novel short-term and long-term regulatory mechanisms that govern
the transition. Finally, our recent results on Methylomicrobium buryatense
5GB1, a promising methanotroph, will be presented, where GEM facilitates
the test of a hypothesis that can explain the observed surprisingly robust
biomass growth under a wide range of culture conditions.

86
TIMING AND COORDINATION OF CELL TYPE RESPONSE
MECHANISMS THAT REGULATE NODULATION

Miriam L Gifford1,2, Beatriz Lagunas1, Mingkee Achom1, Chrysa Sergaki1,

Liam Walker1, Bethany L Richmond1, Proyash Roy1, Patrick Schäfer1,2
1
The University of Warwick, School of Life Sciences, Coventry, United
Kingdom, 2The University of Warwick, Warwick Integrative Synthetic
Biology Centre, Coventry, United Kingdom

Shaping of root architecture is a quintessential developmental response that

involves the concerted action of many different cell types, is highly
dynamic and underpins root plasticity. The influence of the soil
environment, including biotic and abiotic factors, on root system
architecture is similarly dynamic and a particular focus in our work that
studies symbiosis mechanisms. Formation of nodules as a result of cell
division specifically in the legume root cortical cell layer is a developmental
mechanism with intriguing parallels to lateral root development from
pericycle. It follows that biotic and abiotic environmental conditions that
regulate these root developmental programs should be sensed in a highly
cell specific fashion. Our previous work in Arabidopsis using cell type
analysis of the root has shown that individual transcripts are expressed with
a very high degree of temporal and spatial specificity, yet biological
processes are commonly regulated, in a mechanism we term response non-
redundancy. This work highlighted the functional importance of variation in
gene expression timing and location, which can be hypothesized to be
regulated via promoter activity. Within the legume Medicago we have
identified subsets of motifs in the promoters of a multi-gene family
encoding for NCRs (Nodule Cysteine Rich peptides), linked to the circadian
clock. These are commonly considered to play a role as anti-microbial
defensins to keep the rhizobial population in balance, but we suggest their
functions may have diversified

87
APPROACHING GENETIC COMPLEXITY USING FORWARD AND
ASSOCIATION GENETICS

Charlotte Miller1, Qingqing Xie1, Han Wang1, Ling Zhang1, Eric Nguyen1,
Jiahua Zhang1, Qi Yu2, Julian I Schroeder2, Wolfgang Busch1
1
Salk Institute for Biological Studies, Plant Molecular and Cellular Biology
Laboratory, La Jolla, CA, 2University of California, San Diego, Division of
Biological Sciences, Cell and Developmental Biology Section, La Jolla, CA

Complex traits are shaped by the activities of genes that are organized in
gene networks and involve the interactions of multiple genes. While the
ever-growing number of functional genomics datasets are continuously
being used to generate or to refine genome-scale network models, it doesn’t
easily become apparent in which functional context (for instance a growth
response to a specific environmental condition) network modules are
relevant. Together with genetic redundancy, this is likely contributing to the
frequent lack of success of reverse genetics approaches to confirm gene
functions that had been predicted by network approaches. We are
leveraging large-scale phenotyping and phenomics to tackle this
complexity. In our association genetics approach, we use multi-dimensional
root phenotype data in different growth conditions to identify sub-networks
in which genetic variation jointly contributes to the phenotypic variation
observed in natural accessions of Arabidopsis thaliana. With this, we were
able to uncover interesting and novel biological links between molecular
network modules and phenotypic variation of root growth responses to
specific environmental conditions. In a separate approach, we aim to
overcome the challenges posed by genetic redundancy. For this, we conduct
high-throughput screening of a genome-scale collection of multi-gene
artificial-micro RNA based knockdown lines. With this, we were successful
in identifying multiple novel genes involved in root growth responses to
low iron environments.

88
ABIOTIC STRESS RESPONSE IN SHOOT APICAL MERISTEM:
IDENTIFYING GENE REGULATORY NETWORKS THAT LINK
SHOOT MERISTEM DEVELOPMENT AND STRESS RESPONSES

Tie Liu

University of Florida, Horticultural Sciences Department, Gainesville, FL

The Arabidopsis homeobox gene SHOOTMERISTEMLESS (STM) is

essential for formation of the shoot apical meristem and sustained activity.
However, it is very little known about its role in proliferative activities of
the meristems and the coordination between cell division and differentiation
are maintained under environmental stress conditions. Indeed, by analyzing
the downstream targets of STM, we have discovered a number of stress
assoicated genes that are induced by different type of abiotic and biotic
stresses. We use the term stress associated gene to refer to genes with at
least one of the following attributes: genes whose mRNAs (or proteins)
increase in abundance following imposition of a stress such as heat,
drought, salt; genes with high sequence homology to genes implicated in
stress responses in other systems; and genes in which mutations alter the
plant’s stress response. We describe three types of downstream stress-
associated genes activated by STM – the stress responsive transcription
factors (TFs), heat shock proteins, and a member of the Universal Stress
Protein family. Those stress responsive TFs including the membrane
tethered NTM-like, the AP2/ERF, and TCP transcription factors, We are
working on characterizing function of those stress-associated genes as well
as identifying the downstream targets of these stress responsive TFs and
determining what the biological role of these key regulators is in shoot
meristem development. Identification of those abiotic induced genes and
their gene networks could help us understand the regulatory mechanisms
that connect and integrate intrinsic developmental processes with extrinsic
environmental signals during shoot apical meristem and lateral organ
development in plants.

From these studies, we also developed methods and experiments to

understand the mechanisms that plants integrated developmental and
environmental signals in crop plants. We are characterizing the genes that
are involved in stress induced senescence in brassica rapas such as broccoli
using quantitative genetic, genomics, phenomics, and genome-editing
approaches.

89
DEAD ON TIME – MECHANISMS CONTROLLING PROGRAMMED
CELL DEATH IN PLANT DEVELOPMENT

Rafael A Buono1,2, Norbert Bollier1,2, Zongcheng Lin1,2, Marta Cubria

Radio1,2, Anna Daneve1,2, Qiang-Nan Feng1,2, Ellie Himschoot1,2, Maria
Simaskova1,2, Roman Hudecek1,2, Marie L Pfeiffer1,2, Fei Xie1,2, Klaas
Vandepoele1,2, Moritz K Nowack1,2
1
VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium, 2Ghent
University, Department of Plant Biotechnology and Genetics, Ghent,
Belgium

Programmed cell death (PCD) is a fundamental cellular process for the

targeted elimination of cells in multicellular eukaryotes. Animals and plants
utilize different forms of PCD in their immune response, as a reaction to
certain abiotic insults, and as integral part of regular development. A
multitude of developmentally regulated PCD are known in plants, and many
of them are crucial for plant growth and reproduction. Despite its central
role in plant biology, and in contrast to the state of the art in animal and
biomedical research, we know still only little about the molecular regulation
of PCD in plants.
In a comparative approach, we are exploiting several cell death model
systems in Arabidopsis thaliana and maize (Zea mays) to identify core
components of developmentally regulated PCD in plants. Among these
model systems are floral organ senescence, the plant self-incompatibility
response, and development and turnover of the root cap.
We have discovered the first components of central gene regulatory
networks that coordinate cellular differentiation with the preparation and
execution of developmental PCD. Interestingly, several key transcription
factors are able to cause ectopic PCD when inducibly expressed, suggesting
that they are sufficient to control the entire PCD process. Analysis of target
genes has revealed a core set of commonly regulated cell death-activated
genes, many of them encoding hydrolases putatively involved in cell death
execution or post-mortem corpse clearance.
While we are busy investigating aspects of cell death execution particularly
in the root cap model system, we are also keen on further extending our
knowledge of the PCD gene regulatory network in general. In collaboration
with Klaas Vandepoele (VIB-UGent), we are exploiting network modelling
approaches integrating publically available data sets as well as in-house
information generated by bulk- and single-cell RNA sequencing of different
developmental processes in plants. Ultimately, we aim at a comprehensive
understanding of the molecular mechanisms that control preparation and
execution of PCD as a fundamental biological principle in plant
development.

90
NEW INSIGHTS INTO MAIZE EAR DEVELOPMENT USING SINGLE
CELL (sc)RNA-Seq

Xiaosa Xu1, Maggie Crow1, Lei Liu1, Carlos Ortiz-Ramírez2, Liya Wang1,
Doreen Ware1, Kenneth Birnbaum2, Jon Preall1, Jesse Gillis1, David Jackson1
1
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2New York
University, Center for Genomics and Systems Biology, New York, NY

Plant growth and development depends upon meristems, groups of undifferentiated

cells that maintain themselves while initiating new primordia to form leaves,
branches and flowers. In maize, the ear meristem determines its productivity. An
understanding of ear meristem development requires insight into the full diversity of
cell types and developmental domains, and the gene networks required to specify
them. However, these are classified mainly by morphology, as well as by insights
from classical genetics, but this is limited by genetic redundancy and pleiotropy.
High resolution profiles of maize ear development using single cell RNAseq
(scRNAseq) will provide genome wide transcriptional signatures of specific cell
types, and identify highly localized developmental domains involved in maintenance
of plant growth.

We isolated single cells from ear primordia by protoplasting, and used the high-
throughput 10X Genomics Chromium platform to profile 25,000 individual cells
from six independent replicates. We obtained an average of 72,000 sequence reads/
cell, which revealed expression of 2,000 - 3,000 genes/ cell. We detected expression
from 28,000 genes in total, with an average of 5,600 transcripts detected per cell.
Graph-based clustering partitioned cells based on their transcriptomes into 13
groups. Many groups were consistently defined by known markers across all
replicates, such as an L1/epidermal group, marked by OUTER CELL LAYER genes,
an L2 meristem group, marked by KNOTTED1, a primordium group, marked by
YABBY genes, and a vasculature group, marked by RAN BINDING PROTEIN2,
indicating that clusters represented coherent cell identities. Importantly, we also
detected expression of 76 of the 77 known maize inflorescence development genes
defined by mutant phenotype, and every one of them had enriched expression in one
or more of the 13 clusters. Remarkably, we are also able to capture lowly expressed
stem-cell marker genes, such as Zea mays CLAVATA3/EMBRYO SURROUNDING
REGION7 (ZmCLE7). In addition, each group contained an additional ~20-200 new
candidate cell type or domain specific markers. We validated our findings using
Fluorescence Activated Cell Sorting (FACS) of reporter lines, such as pYABBY14-
TagRFPt, and found a highly significant overlap between genes enriched in FACS
and in YABBY scRNAseq clusters. We also localized each cell population using in
situ hybridization for selected marker genes, and found specific, spatially restricted
markers in each group. Strikingly, we also identified novel markers for specific
developmental domains, such as meristem tips and meristem branching sites.
Mutants of candidate marker genes and their co-expressed paralogs are being
generated by multiplex CRISPR/CAS9 to test the hypothesis that these genes control
maize ear development.

Collectively, we demonstrate that scRNA-seq offers for the first time the
opportunity to profile tens of thousands of maize ear inflorescence cells, and
identified hundreds of novel regulators of cell fate to understand plant development
at a fundamentally new level. (Funded by the NSF)

91
THE ARABIDOPSIS TIR1/AFB AUXIN RECEPTOR GENES HAVE
BOTH OVERLAPPING AND SPECIALIZED FUNCTIONS

Michael Prigge1, Matthieu Platre2, Wolfgang Busch2, Mark Estelle1

1
UCSD, Cell and Developmental Biology, La Jolla, CA, 2The Salk Institute,
La Jolla, CA

The TIR1/AFB auxin co-receptors mediate diverse responses to the plant

hormone auxin. The Arabidopsis genome encodes six TIR1/AFB proteins
representing three of the four clades that were established prior to
angiosperm radiation. To determine the role of these proteins in plant
development we performed an extensive genetic analysis involving the
generation and characterization of all  possible  multiply mutant lines.
Although the three  major subclades were established  approximately
 400 MYA, our genetic studies reveal that  for most auxin-regulated growth
processes, the TIR1/AFB proteins  retain  largely overlapping functions.
The loss of all six proteins results in defects in embryogenesis as early as
the first division of the apical cell. Mutant embryos progress but exhibit
frequent cell division errors and proliferation of the suspensor. Despite this
dramatic phenotype, a single wild-type allele of  TIR1 or  AFB2  is
sufficient to support growth  throughout  plant development in lab
conditions. Further, our studies indicate that gametophytic expression of
TIR1/AFB genes is not essential for development of the male or female
gametophyte. Finally, we show that the AFB1 protein has a specialized
function in rapid auxin inhibition of root growth.

92
CROSS-KINGDOM RNAi AND SMALL RNA TRAFFICKING
BETWEEN PLANTS AND FUNGAL PATHOGENS

Qiang Cai, Baoye He, Shumei Wang, Hailing Jin

University of California, Riverside, Department of Microbiology & Plant

Pathology, Center for Plant Cell Biology, Institute for Integrative Genome
Biology, Riverside, CA

Small RNAs (sRNAs) are a class of short non-coding RNAs that mediate
gene silencing in a sequence-specific manner. We have demonstrated that
some sRNAs from eukaryotic pathogens, such as Botrytis cinerea, the
fungal pathogen that causes grey mold disease on more than 1000 plant
species, can be transported into host plant cells and suppress host immunity
genes for successful infection (Weiberg et al., Science 2013). We recently
discovered that such cross-kingdom RNAi is bi-directional. Plants can also
send small RNAs into pathogens using extracellular vesicles to silence
fungal virulence genes as part of its immune responses (Cai et al., Science
2018). We found that plants have multiple classes of extracellular vesicles,
and exosome-like vesicle is the major class responsible for sRNA delivery.

Furthermore, we also discovered that many fungal pathogens, such as B.

cinerea, can take up double-stranded RNAs and sRNAs from the
environment. Applying sRNAs or dsRNAs that target Botrytis Dicer genes
on the surface of fruits, vegetables and flowers significantly inhibits grey
mold disease (Wang et al,, Nature Plants, 2016). Such pathogen gene-
targeting RNAs represent a new generation of fungicides that are durable
and eco-friendly.

References
[1] Arne Weiberg, Ming Wang, Feng-Mao Lin, Hongwei Zhao, Zhihong
Zhang, Isgouhi Kaloshian, Hsien-Da Huang, Hailing Jin*: Fungal small
RNAs suppress plant immunity by hijacking host RNA interference
pathways. Science, 2013, 342 (6154) 118-123.
[2] Qiang Cai, Lulu Qiao, Ming Wang, Baoye He, Feng-Mao Lin, Jared
Palmquist, Hsien-Da Huang, and Hailing Jin*: Plants send small RNAs in
extracellular vesicles to fungal pathogen to silence virulence genes. Science,
2018, 360(6393)1126-1129.
[3] Ming Wang, Arne Weiberg, Feng-Mao Lin, Bart P. H. J. Thomma,
Hsien-Da Huang and Hailing Jin*: Bidirectional cross-kingdom RNAi and
fungal uptake of external RNAs confer plant protection. Nature Plants,
2016, 10.1038/nplants.2016.151.

93
A NEW LONG-READ SEQUENCING PLATFORM FOR GENOME
ASSEMBLY

Solomon Endlich, Ashby J Morrison

Base5 Genomics, Inc, Plant Genomics Division, Menlo Park, CA

Plant genomes often represent unique challenges for assembly, as many

have repetitive sequences and elevated ploidy. Current methodologies for
genome assembly utilize a combination of short-read (Illumina) and long-
read (PacBio, Nanopore) sequencing technologies. While long-read
sequencing assists in mapping low-complexity repetitive regions, it often
suffers from reduced accuracy, thus the need for high-accuracy short-reads.
Base5 Genomics has developed a new long-read sequencing technology that
utilizes short-read sequencers to create high-accuracy synthetic long-reads.
We expect this new approach to greatly facilitate assembly of complex
genomes.

94
ENGINEERING PLANT DEVELOPMENT TO CONTROL ROOT
SHAPE

Jennifer A Brophy1,2, Katie J Magallon1,2, Jose R Dinneny1,2

1
Stanford University, Biology, Stanford, CA, 2Carnegie Institution for
Science, Plant Biology, Stanford, CA

The shape of a plant’s root system influences its ability to reach essential
nutrients in the soil and to acquire water during drought. Progress in
engineering plant roots to optimize water and nutrient acquisition has been
limited by our capacity to design and build genetic programs that alter root
growth in a predictable manner. Synthetic genetic circuits that enable
precise spatial, temporal, and magnitudinal control over gene expression
offer an exciting means to reprogram plant development and control root
growth. However, limited tools currently exist for constructing synthetic
genetic circuits in plants. We generated a collection of synthetic regulatory
parts (promoters, transcriptional activators, transcriptional repressors) to
control gene expression in plants and have used them to construct simple
dynamic circuits and logic gates. These genetic circuits are now being used
to regulate spatial and temporal expression patterns of developmental
transcription factors to predictably alter root structure. We show that
specific changes to root branching can be achieved by precisely controlling
spatial patterns of gene expression.

95
UNRAVEL STRIGOLACTONE SIGNALING AND CONTROLLING
PARASITIC PLANT BEHAVIORS WITH SMALL MOLECULES

Yuichiro Tsuchiya

Nagoya University, Institute of Transformative Bio-Molecules, Nagoya,

Japan

Striga hermonthica (Striga) parasitizes crops widely across various parts of

sub-Saharan Africa, causing loss in crop yields that result in economic
pressure on millions of smallholder farmers and lead to annual losses of
billions of dollars. As Striga seeds require host-generated strigolactones
(SLs) to germinate, understanding the mechanism of SL signaling could
lead the development of chemical agent for controling these noxious weeds.
We have been approaching to the problem with small moelcule probes
including a fluorotgenic probe for SL receptors called yoshimulactone green
which is designed to fluoresce only when it is perceived by the receptors
(Tsuchiya and Yoshimura et al., Science, 2015). Yoshimulactone green
allowed us not only to identify the 11 members of SL receptors, but also to
visualize a dynamic wave-like pattern of SL perception in Striga seeds.
These discoveries accerelated our research for the development a femto-
molar range germination stimulants for Striga (Uraguchi et al., Science,
2018). The stimulant called sphynolactone-7 is expected to be used as an
inducer of “suicide germination” to Striga; inducing Striga seed
germination without host plants leads the seeds to die within 4 days. In this
seminar, I will present how chemical biology approach contributes to
understanding this serious problem and developing lead compounds to
combat against Striga.

96
THE CIS-REGULATORY LANDSCAPE OF MAIZE SINGLE CELLS

Alexandre P Marand, Zefu Lu, Xiaoyu Zhang, Robert J Schmitz

University of Georgia, Department of Genetics, Athens, GA

Complex tissues are comprised of distinct cell-types programmed to carry

out highly specialized functions that collectively determine phenotypic
manifestation of a multicellular organism. The genomic blueprints encoding
cellular function are provided by non-coding sequences called cis-
regulatory elements (CREs). We implemented single-cell sequencing of
Assay for Transposase Accessible Chromatin (scATAC-seq) in Zea mays to
document the comprehensive catalog of CREs essential for establishing
cellular identity and progression through developmental trajectories. We
characterize patterns of differential chromatin accessibility in more than
33,000 single cells comprising four major tissues. Classifying and aligning
cells to a pseudotime trajectory of cell cycle uncovered the temporal
regulatory program of cycle progression in distinct cell clusters and tissues.
Analysis of co-accessible chromatin readily recapitulated known and novel
high-order chromatin interactions on a per cell-cluster basis, providing
novel insight into cell type-specific regulatory dynamics. Combinatorial
accessibility of unique transcription factor (TF) binding sites coincided with
discrete grouping of cells based on patterns of chromatin accessibility,
suggesting differential accessibility of TF binding sites underlies cell state
identity. We demonstrate that single cells in maize exhibit pervasive cis-
regulatory variation and establish an analytical framework for decoding
regulatory function for a diverse array of distinct cell-types.

97
BREAKTHROUGHS IN PLANT BASED PHB PRODUCTION:
HARNESSING NATURE TO HEAL NATURE

Kristi D Snell1, Meghna Malik2, Oliver P Peoples1

1
Yield10 Bioscience, Inc., Woburn, MA, 2Metabolix Oilseeds, Inc.,
Saskatoon, Saskatchewan, Canada

Crops have the potential to not only be a source of food and fuel but also a
source of renewable materials. One of the most interesting classes of
material targets are the polyhydroxyalkanoate (PHA) family of microbial
carbon and energy storage polymers, which have a wide range of potential
applications. Although PHAs are targeted as replacements for petroleum
derived plastics, and over time these markets will dominate, water treatment
is a simpler market entry strategy and directly linked to improving the
sustainability of food production and consumption. PHAs are well known
growth-substrates for denitrifying bacteria in water systems enabling them
to convert nitrate to nitrogen gas and reduce nitrate levels produced from
food production and human waste. Developing PHA producing oilseed
cover crops such as Camelina sativa to reduce nitrogen runoff in
agricultural fields would also enable low cost production of PHA pellets for
water treatment applications. Oilseeds are an ideal production platform
since seed metabolism is well suited to the polymer pathways and multiple
co-products can be harvested (polymer, seed oil, protein rich seed meal)
increasing the value of the seed.

Yield10 has made significant progress in addressing the technical

challenges of producing polyhydroxybutyrate (PHB), the simplest member
of the PHA family, in plants. We previously demonstrated the production of
high levels of PHB in the seeds of Camelina by targeting enzymes for PHB
synthesis to the seed plastids, however the seedlings were severely impaired
in emergence and survival. Yield10 has recently demonstrated a cytosolic
PHB production pathway with an ER targeted polymerizing enzyme PHA
synthase that produced PHB levels up to 10.2% of the seed weight in T4
seeds with good seedling emergence and survival. These results are a
significant step forward towards commercial production of PHB in plants.

98
NOTES
NOTES
NOTES
NOTES
NOTES
NOTES
Participant List
Dr. Bradley Abramson Dr. Philippa Borrill
J. Craig Venter Institute University of Birmingham
[email protected] [email protected]

Dr. Amir Ahkami Dr. Zachary Brenton

Pacific Northwest National Laboratory Clemson University
[email protected] [email protected]

Ms. Burcu Alptekin Dr. Jennifer Brophy

Montana State University Stanford University
[email protected] [email protected]

Dr. Siwaret Arikit Dr. Wolfgang Busch

Kasetsart University Salk Institute
[email protected] [email protected]

Mr. Oliver Artz Dr. ZONG-MING CHENG

Cold Spring Harbor Laboratory University of Tennessee, USA and Nanjing
[email protected] Agricultural University, China
[email protected]
Dr. Mentewab Ayalew
Spelman College Mr. Kapeel Chougule
[email protected] Cold Spring Harbor Laboratory
[email protected]
Dr. Yang Bai
Cornell University Dr. Kate Creasey
[email protected] Grow More Foundation
[email protected]
Ms. Morgan Bennett
University of Tennessee Dr. Josh Cuperus
[email protected] University of Washington
[email protected]
Dr. Wajid Bhat
Michigan State University Dr. Geert De Jaeger
[email protected] VIB-Ghent University
[email protected]
Prof. Frederik Boernke
Leibniz-Institute Grossbeeren (IGZ) Dr. Augusto Diniz
[email protected] Cold Spring Harbor Laboratory
[email protected]
Dr. Mark Estelle Dr. Yuzhao Hu
UCSD Cold Spring Harbor Laboratory
[email protected]

Dr. Georg Jander

Ms. Tina Ethridge
Boyce Thompson Institute for Plant
University of Georgia
Research
[email protected]
[email protected]

Dr. Leila Feiz

Dr. Yinping Jiao
Boyce Thomson Institute, Cornell University
Cold Spring Harbor Laboratory
[email protected]
[email protected]

Dr. Joseph Gallagher

Dr. Hailing Jin
University of Massachusetts-Amherst
University of California, Riverside
[email protected]
[email protected]

Dr. Mary Gehring

Dr. Tobias Jores
Whitehead Institute for Biomedical
University of Washington
Research
[email protected]
[email protected]

Ms. Kumud Joshi

Dr. Miriam Gifford
Bowling Green State University
University of Warwick
[email protected]
[email protected]

Mr. Russell Julian

Dr. Nicholas Gladman
Purdue University
Cold Spring Harbor Laboratory
[email protected]
[email protected]

Dr. Joseph Kawash

Dr. Hardeep Gumber
ORISE - USDA
Cold Spring Harbor Laboratory
[email protected]
[email protected]

Dr. Sun A Kim

Dr. Cara Haney
Dartmouth College
University of British Columbia
[email protected]
[email protected]

Mr. Kyung mo Kim

Dr. Jim Haseloff
Stony Brook University
University of Cambridge
[email protected]
[email protected]

Prof. Per Kjellbom

Dr. Venura Herath
Lund University
Texas A&M University
[email protected]
[email protected]
Mr. Harry Klein Dr. Zachary Lippman
University of Massachusetts Amherst Cold Spring Harbor Laboratory
[email protected] [email protected]

Dr. Arthur Korte Dr. Tie Liu

University Wuerzburg University of Florida
[email protected] [email protected]

Dr. Ute Krämer Mr. Zhenyuan Lu

Ruhr University Bochum Cold Spring Harbor Laboratory
[email protected] [email protected]

Dr. Ksenia Krasileva Dr. Ulrich Lutz

University of California Berkeley Max Planck Institute for Developmental
[email protected] Biology
[email protected]
Dr. Vivek Kumar
Cold Spring Harbor Laboratory Ms. Erika Magnusson
[email protected] University of Minnesota
[email protected]
Dr. Benoit Lacombe
CNRS Mr. Jarrett Man
[email protected] University of Massachusetts Amherst
[email protected]
Dr. Jesse Lasky
Pennsylvania State University Dr. Alexandre Marand
[email protected] University of Georgia
[email protected]
Dr. Miaomiao Li
NYU Dr. Cristina Marco
[email protected] Cold Spring Harbor Laboratory
[email protected]
Marc Libault
University of Nebraska Lincoln Dr. Richard McCombie
[email protected] Cold Spring Harbor Laboratory
[email protected]
Mr. YI-CHEN LIN
Max Planck Institute for Plant Breeding Dr. Richard McCombie
Research Cold Spring Harbor Laboratory
[email protected] [email protected]

Dr. Yao-Cheng Lin Dr. Devang Mehta

Academia Sinica University of Alberta
[email protected] [email protected]
Ms. Sendi Meja Dr. Ron Ophir
Cold Spring Harbor Laboraty Agricultural Research Organization
[email protected] [email protected]

Mr. John Mendieta Dr. Donald Ort

University of Georgia University of Illinois
[email protected] [email protected]

Dr. Raphael Mercier Dr. Jane Parker

Max Planck Institute for Plant Breeding Max-Planck Institute for Plant Breeding
Research Research
[email protected] [email protected]

Prof. Ashby Morrison Dr. Anna Piasecka

Stanford University Polish Academy of Sciences
[email protected] [email protected]

Mr. Peter Morrison Dr. Anahid Powell

University of Warwick Adelphi University
[email protected] [email protected]

Mr. Shuai Mu Dr. Simona Radutoiu

Dartmouth college Aarhus University
[email protected] [email protected]

Mr. Radesh Nattamai Malli Dr. Satyaki Rajavasireddy

Pooranachandhiran Whitehead Institute for Biomedical
Brock University Research
[email protected] [email protected]

Dr. Ross Nazar Dr. Sue (Seung) Rhee

University of Guelph Carnegie Institution for Science
[email protected] [email protected]

Dr. Cuong Nguyen Ms. Kanamon Riangwong

University of Missouri Graduate Program in Genetic Engineering
[email protected] [email protected]

Dr. Moritz Nowack Mr. William Ricci

Ghent University University of Georgia
[email protected] [email protected]
Dr. Jane Robb Dr. Anne Simon
University of Guelph University of Maryland
[email protected] [email protected]

Dr. Jessica Rodrigues Dr. Joseph Simorowski

New Zealand Institute for Plant and Food Cold Spring Harbor Laboratory
Research [email protected]
[email protected]
Dr. Yana Sindarovska
Dr. Jacques Rouster Institute of Cell Biology and Genetic
BIOGEMMA Engineering
[email protected] [email protected]

Dr. Elizabeth Sattely Dr. Kristi Snell

Stanford University Yield10 Bioscience
[email protected] [email protected]

Dr. Aneta Sawikowska Dr. Shyam Solanki

Polish Academy of Sciences/University of Washington State University
Life Scie [email protected]
[email protected]
Dr. Liang Song
Dr. Meredith Schuman University of British Columbia
University of Zurich [email protected]
[email protected]
Dr. Olya Spassibojko
Dr. Samuel Seaver Cold Spring Harbor Laboratory
Argonne National Laboratory [email protected]
[email protected]
Ms. Thanvi Srikant
Dr. Gothandapani Sellamuthu Max Planck Institute for Developmental
M S Swaminathan Research Foundation Biology
[email protected] [email protected]

Dr. Amir Sherman Dr. Kathryn Storey

ARO Canadian Food Inspection Agency
[email protected] [email protected]

Dr. Patrick Shih Dr. Milos Tanurdzic

University of California, Davis The University of Queensland
[email protected] [email protected]
Dr. Marcela Tello-Ruiz Dr. Detlef Weigel
Cold Spring Harbor Laboratory Max Planck Institute for Developmental
[email protected] Biology
[email protected]
Dr. Yuichiro Tsuchiya
Nagoya University Dr. Ben Williams
[email protected] Whitehead Institute for Biomedical
Research
Dr. Walter Verweij [email protected]
ENZA zaden R&D
Dr. Xiaosa Jack Xu
[email protected]
Cold Spring Harbor Laboratory
Dr. Kamaldeep Virdi [email protected]
University of Nebraska Lincoln
Prof. Shuqing Xu
[email protected]
Institute for Evolution and Biodiversity
Dr. John Vogel [email protected]
DOE Joint Genome Institute
Dr. JOSE ZAMBRANO
[email protected]
Lund University
Dr. Jin Wang [email protected]
Auburn
Dr. Lifang Zhang
[email protected]
Cold Spring Harbor Laboratory
Dr. Bo Wang [email protected]
Cold Spring Harbor Lab
Dr. Jin Zhang
[email protected]
Oak Ridge National Laboratory
Dr. Liya Wang [email protected]
Cold Spring Harbor Laboratory
Ms. YINWEN ZHANG
[email protected]
UNIVERSITY OF GEORGIA
Dr. Doreen Ware [email protected]
Cold Spring Harbor Laboratory/USDA/ARS
Dr. Kangmei Zhao
[email protected]
Carnegie Institute for Science
Ms. Wei Wei [email protected]
University of Illinois
Dr. CHENG ZHAO
[email protected]
Carnegie Institude for Science
Dr. Sharon Wei [email protected]
Cold Spring Harbor Laboratory
[email protected]
Dr. Jian-Min Zhou
Institute of Genetics and Developmental
Biol, CAS
[email protected]

Dr. Jiaying Zhu

Carnegie Institution for Science
[email protected]
 VISITOR INFORMATION

EMERGENCY CSHL BANBURY

Fire (3) 742-3300 (3) 692-4747
Ambulance (3) 742-3300 (3) 692-4747
Poison (3) 542-2323 (3) 542-2323
Police (3) 911 (3) 549-8800
Safety-Security Extension 8870

Emergency Room 631-351-2000

Huntington Hospital
270 Park Avenue, Huntington
Dentists
Dr. William Berg 631-271-2310
Dr. Robert Zeman 631-271-8090
Doctor 631-423-5400
MediCenter
234 W. Jericho Tpke., Huntington Station
Drugs - 24 hours, 7 days 631-549-9400
Rite-Aid
391 W. Main Street, Huntington

GENERAL INFORMATION

Books, Gifts, Snacks, Clothing, Newspapers

BOOKSTORE 367-8837 (hours posted on door)
Located in Grace Auditorium, lower level.

Photocopiers, Journals, Periodicals, Books, Newspapers

Photocopying – Main Library
Hours: 8:00 a.m. – 9:00 p.m. Mon-Fri
10:00 a.m. – 6:00 p.m. Saturday
Helpful tips – Use PIN# 57305 to enter Library after hours.
See Library staff for photocopier code.

Computers, E-mail, Internet access

Grace Auditorium
Upper level: E-mail and printing in the business center area
STMP server address: mail.optonline.net
To access your E-mail, you must know the name of your
home server.

Dining, Bar
Blackford Hall
Breakfast 7:30–9:00, Lunch 11:30–1:30, Dinner 5:30–7:00
Bar 5:00 p.m. until late (Cash Only)
Helpful tip - If there is a line at the upper dining area, try the
lower dining room

Messages, Mail, Faxes, ATM

Message Board, Grace, lower level
Swimming, Tennis, Jogging, Hiking
June–Sept. Lifeguard on duty at the beach. 12:00 noon–6:00 p.m.
Two tennis courts open daily.

Russell Fitness Center

Dolan Hall, east wing, lower level
PIN#: Press 57305 (then enter #)

Meetings & Courses Front Office

Hours during meetings: 8am – 7pm, until 9pm on arrival day
After hours – From guest house phones, dial x8870 for
assistance

Pay Phones, House Phones

Grace, lower level; Cabin Complex; Blackford Hall; Dolan Hall,
foyer

CSHL’s Green Campus

Cold Spring Harbor Laboratory is pledged to operate in an

environmentally responsible fashion wherever possible. In the past,
we have removed underground oil tanks, remediated asbestos in
historic buildings, and taken substantial measures to ensure the
pristine quality of the waters of the harbor. Water used for irrigation
comes from natural springs and wells on the property itself. Lawns,
trees, and planting beds are managed organically whenever
possible. And trees are planted to replace those felled for
construction projects.

Two areas in which the Laboratory has focused recent efforts have
been those of waste management and energy conservation. The
Laboratory currently recycles most waste. Scrap metal, electronics,
construction debris, batteries, fluorescent light bulbs, toner cartridges,
and waste oil are all recycled. For general waste, the Laboratory
uses a “single stream waste management” system, removing
recyclable materials and sending the remaining combustible trash to a
cogeneration plant where it is burned to provide electricity, an
approach considered among the most energy efficient, while
providing a high yield of recyclable materials.

Equal attention has been paid to energy conservation. Most lighting

fixtures have been replaced with high efficiency fluorescent fixtures,
and thousands of incandescent bulbs throughout campus have been
replaced with compact fluorescents. The Laboratory has also
embarked on a project that will replace all building management
systems on campus, reducing heating and cooling costs by as much
as twenty-five per cent.

Cold Spring Harbor Laboratory continues to explore new ways in

which we can reduce our environmental footprint, including
encouraging our visitors and employees to use reusable containers,
conserve energy, and suggest areas in which the Laboratory’s efforts
can be improved. This book, for example, is printed on recycled
paper.
 1-800 Access Numbers

AT&T 9-1-800-321-0288

Local Interest
Fish Hatchery 631-692-6758
Sagamore Hill 516-922-4788
Whaling Museum 631-367-3418
Heckscher Museum 631-351-3250
CSHL DNA Learning x 5170
Center

New York City

Helpful tip -
Take Syosset Taxi to Syosset Train Station
($9.00 per person, 15 minute ride), then catch Long Island
Railroad to Penn Station (33rd Street & 7th Avenue).
Train ride about one hour.

TRANSPORTATION
Limo, Taxi
Syosset Limousine 516-364-9681
Executive Limo Service 631-696-8000
Super Shuttle 800-957-4533
Limos Long Island 833-545-4667,ext.3

To head west of CSHL - Syosset train station

Syosset Taxi 516-921-2141
To head east of CSHL - Huntington Village
Orange & White Taxi 631-271-3600

Trains
Long Island Rail Road 822-LIRR
Schedules available from the Meetings & Courses Front Office.
Amtrak 800-872-7245
MetroNorth 877-690-5114
New Jersey Transit 973-275-5555

Ferries
Bridgeport / Port Jefferson 631-473-0286
Orient Point/ New London 631-323-2525

Car Rentals
Avis 631-271-9300
Enterprise 631-424-8300
Hertz 631-427-6106

Airlines
American 800-433-7300
British Airways 800-247-9297
Delta 800-221-1212
Japan Airlines 800-525-3663
Jet Blue 800-538-2583
KLM 800-374-7747
Lufthansa 800-645-3880
Southwest Airlines 800-435-9792
United 800-241-6522
Virgin American 877-359-9792
 Code of Conduct

Cold Spring Harbor Laboratory is dedicated to pursuing its twin missions of

research and education in the biological sciences. The Laboratory is
committed to fostering a working environment that encourages and supports
unfettered scientific inquiry and the free and open exchange of ideas that are
the hallmarks of academic freedom. The Laboratory aims to maintain a safe
and respectful environment for all attendees of our meetings and courses
and associated support staff, by providing an environment free from
discrimination and harassment, in accordance with federal, state, and local
laws.

Consistent with the Laboratory's missions, commitments and policies, the

purpose of this Code is to set forth the Laboratory's expectations for the
professional conduct of individuals participating in the Laboratory's meetings
program, including organizers, session chairs, invited speakers, presenters,
attendees and sponsors.

By attending a CSHL meeting, participants agree to:

1. Treat fellow meeting participants and CSHL staff with respect, civility
and fairness, and without bias based on race, color, religion, sex,
national origin, citizenship status, sexual orientation, gender identity or
expression, age, disability, marital status, veteran status, genetic
information, or any other criteria prohibited under applicable federal,
state or local law.

2. Use all CSHL facilities, equipment, computers, supplies and resources

responsibly and appropriately, as you would at your home institution.

Meeting participants agree to refrain from:

1. Discrimination in violation of Laboratory policy based on age, gender,

race, ethnicity, national origin, religion, disability, or sexual orientation.

2. Behavior that is disrespectful of others, and unprofessional

interpersonal behavior that interferes with the working and learning
environment.

3. Unwanted physical contact with others, or threats of such contact.

4. Sexual harassment or harassment based on age, gender, race,

ethnicity, national origin, religion, disability or sexual orientation.

5. Loss of civility that interferes with the working and learning environment
(for example shouting, personal attacks or insults, throwing objects or
other displays of temper).

6. Misappropriation of Laboratory property or excessive personal use of

resources.
 Breaches or Violations of the Code of Conduct

Cold Spring Harbor Laboratory aims to maintain a conference environment

in accordance with the principles and expectations outlined in the Code of
Conduct. Meeting organizers are tasked with providing leadership during
each meeting, and may be approached informally about any breach or
violation. Breaches or violations should also be reported to program
leadership in person or by email:

 Dr. David Stewart, Grace Auditorium Room 204, 516-367-8801 or

x8801 from a campus phone, [email protected]

 Dr. Charla Lambert, Hershey Laboratory Room 214, 516-367-5058

or x5058 from a campus phone, [email protected]

The Laboratory will take action as needed to resolve the matter, up to and
including immediate expulsion of the offending participant(s) from the
meeting, dismissal from the Laboratory, and exclusion from future academic
events offered by CSHL.