Omics sciences in agriculture: Crop phenomes and microbiomes

Omics sciences in agriculture : crop phenomes and microbiomes / Andres Jaramillo-Botero,Carlos Arango Mambuscay, Jaime Aguilar-Zambrano, editors. -- Santiago de Cali : Pontificia Universidad Javeriana, Sello Editorial Javeriano, 2023.

164 pages: illustrations ; 24 cm

Includes bibliographical references.

ISBN paperback: 9786287618572

ISBN e-book: 9786287618589

1. Phenotype 2. Agronomic characteristics 3. Genetic phenomena 4. Genotype -- Environment interaction 3. Agricultural innovations -- Research 2. Agriculture -- Technology transfer 3. Food security -- Technological innovations -- Research 5. Sugarcane -- Crops -- Technological innovations 6. Rice -- Crops -- Technological innovations I. Jaramillo-Botero, Andres, editor II. Arango, Carlos, editor III. Aguilar-Zambrano, Jaime, editor IV. Pontificia Universidad Javeriana Cali. Vicerrectoría Académica. Instituto de Investigación en Ciencias Ómicas - iÓmicas

SCDD 576.53 ed. 23

COCaPUJ

lmc/2023

Omics sciences in agriculture:

crop phenomes and microbiomes

Instituto de Investigación en Ciencias Ómicas-iÓmicas

Vicerrectoría Académica

Editors:

Andres Jaramillo-Botero

Carlos Alberto Arango Mambuscay

Jaime Aguilar-Zambrano

Authors:

Fernando Gordillo-Delgado

Julián David Arbeláez Moreno

Daniel Felipe Casas Castañeda

Marwin J.M Jiménez

Andres Jaramillo-Botero

Alba Ávila

Wilyereny Lorenzo Placencio

George Báez Beltré

Margari Pérez Collantes

Willy M. Maurer

Daniela Tamayo Jaramillo

Sergio Alejandro González Quintana,

Laura Isabel Gil Pineda

Carlos Alberto Arango Mambuscay

Sara Lizeth Cuellar Ospina

Jhon Freddy González-Álvarez

Andrés F. Jr Duque

Ingrid Z. Casallas

Edgar S. Correa

Francisco Calderón

Eliel Petro

Maria C. Rebolledo

Natalia Espinosa

Nelson Amezquita

Oscar D. Puentes

Diego A. Patiño

Iván F. Mondragón

Julián D. Colorado

Diego González-Bello

Alejandro Caro Quintero

Michael Gribskov

Esperanza Torres-Rojas

Wendy Ríos-Guzmán

Emiliano Barreto-Hernández

Andres Jaramillo-Botero

Jaime Aguilar-Zambrano

Scientific Committee:

Jaime Aguilar-Zambrano, PhD, Pontificia Universidad Javeriana Cali

Gloria Álvarez, PhD, Pontificia Universidad Javeriana Cali

Alba Ávila, PhD, Universidad de los Andes

Hernán Benítez, PhD, Pontificia Universidad Javeriana Cali

Paola Caicedo, PhD, Universidad Icesi

Manuel Chaur, PhD, Universidad de Valle

Julián Colorado, PhD, Pontificia Universidad Javeriana Bogotá

Andrés Davalos, PhD, Universidad Icesi

Andrés Escorcia, PhD, Universidad Icesi

Gerardo Fontal, PhD, Universidad del Quindío

Víctor García, PhD, Universidad del Quindío

Thaura Ghneim, PhD, Universidad Icesi

Nicolas Gil, PhD, Cenicaña

Andres Jaramillo-Botero, PhD, California Institute of Technology, Pontificia Universidad Javeriana Cali

José Guillermo López, PhD, Universidad del Valle

Alexander Martínez, PhD, Pontificia Universidad Javeriana Cali

Ana Teresa Mosquera, PhD, Pontificia Universidad Javeriana Cali

Fernando Muñoz, PhD, Cenicaña

Julián Másmela, PhD, Cenicaña

Lizeth Pérez, PhD, Universidad Icesi

Irina Peña, PhD, Pontificia Universidad Javeriana Cali

Duina Posso, PhD, Pontificia Universidad Javeriana Cali

Mauricio Quevedo, PhD, Cenicaña

Carlos Alberto Arango Mambuscay, PhD, Universidad Icesi

Mauricio Alberto Quimbaya Gómez, PhD, Pontificia Universidad Javeriana Cali

Camilo Rocha, PhD, Pontificia Universidad Javeriana Cali

Giovanni Rojas, PhD, Universidad Icesi

Marcela Santaella, PhD, CIAT

Eugenio Taruma, PhD, Pontificia Universidad Javeriana Cali

Liliana Tirado-Mejía, PhD, Universidad del Quindío

Fabian Tobar, PhD, Pontificia Universidad Javeriana Cali

Luis Tobón, PhD, Pontificia Universidad Javeriana Cali

John Trujillo, PhD, Cenicaña

Drochss Valencia, PhD Pontificia Universidad Javeriana Cali

Hernán Vargas, PhD Pontificia Universidad Javeriana Cali

Gerardo Fontal, PhD Universidad del Quindío

Roger Gómez, PhD Universidad Icesi

ISBN: 978-628-7618-57-2

ISBN(e): 978-628-7618-58-9

Format: 17 x 24 cms

Rector: Vicente Durán Casas S.J.

Academic vicerector: Ingrid Schuler García

Editorial coordination: Claudia Lorena González González

Editorial assistant: Jennifer Ramírez Martínez

Editorial design: Kevin Nieto Vallejo

Front cover: Ariadna Ángel Rodríguez

Style correction: Comunicaciones Creativas

Print: Carvajal Soluciones de Comunicación S.A.S

Pontificia Universidad Javeriana Cali

Calle 18 N°118-250

Teléfonos (57-2) 3218200

Santiago de Cali, Colombia, 2023

The content of this publication is the sole responsibility of its author and does not compromise the Institution’s thinking. This book may not be reproduced by any print or reproducible media without written permission from the copyright holders.

Preface

Introduction:

Assessment of Morphological and Physiological Characters for Phenotyping of Three Varieties of Sugarcane (Saccharum Officinarum: Poaceae)

I. INTRODUCTION

II. MATERIALS AND METHODS

III. RESULTS AND DISCUSSION

IV. CONCLUSIONS

REFERENCES

Graph Subspace Fusion from Super-Pixels for Biomass Estimation in Rice Crops

I. Introduction

II. Graph Signal Smoothness Prior Graph Learning

III. Graph Subspace Fusion

IV. Experimental results and discussion

V. Conclusions

VI. References

A Colorimetric Sensor for Detection of Aluminum (III) using Gold Nanoparticles

I. Introduction

II. Experimental section

III. Results and Discussion

IV. Conclusions

V. References

Optimization of irrigation in CL-86 maize production using data mining and machine learning

I. INTRODUCTION

II. Data Collection

III. Data analysis

IV. Algorithm

V. CONCLUSIONS

VI. REFERENCES

Geometrical-Probabilistic Approach to Protein Secondary Structure Assignment

I. Introduction

II. Theory and Methods

III. Performance of

kt

S²

IV. Results and analysis

V. Conclusions and perspectives

VI. Statements and Declarations

VII. Data and Software Availability

VIII. References

Photoacoustic monitoring of Gros Michel banana seedlings infected with Fusarium oxysporum F. SP cubense Race 1

I. Introduction

II. Materials and methods

III. Results and discussion

IV. Conclusions

V. References

Classification of Rice Genotypes Using Features from UAV-Acquired Above-Ground Multispectral Imagery

I. Introduction

II. Methods

III. Results

IV. Conclusions

V. References

Analysis of fungal microbiome present in cacao soils containing natural cadmium

I. INTRODUCTION

II. MATERIALS AND METHODS

III. RESULTS

IV. DISCUSSION

V. REFERENCES

Characterization of bacterial microbiomes present in cacao soils with cadmium in Cundinamarca-Colombia

I. INTRODUCTION

II. MATERIALS AND METHODS

III. RESULTS

VI. DISCUSSION

V. REFERENCE

The In-silico Multiscale Optimization of Sustainable Agricultural Crops Alliance (Ómicas) is part of the Colombian scientific ecosystem. Ómicas is a research alliance involving more than 300 researchers from 17 institutions spread across four continents. It focuses on developing, validating, and deploying new scientific and technological solutions to effectively address humanity’s overarching challenges in food security and sustainable agricultural production worldwide.

Ómicas focuses on the omics characterization of plant organisms to optimize their productivity despite increasing stressors of biotic and abiotic origin. The field of omics science, from the genome to the phenome, has become increasingly important in modern agriculture research. By characterizing and studying the molecular building blocks of plant systems, we have better understood how they respond to different environmental stresses, such as drought, heat, salinity, and diseases. This has significantly reduced the time and cost of breeding varieties with improved traits.

We now use whole genome sequencing, transcriptomics, proteomics, metabolomics, and phenomics to uncover the molecular processes underlying plant growth, development, and environmental response. This has enabled the development of crop varieties more resistant to environmental stressors, resulting in higher and more stable yields under adverse conditions.

In addition to enhancing crop productivity, omics science is now allowing us to focus on the nutritional quality of crops, which has significant implications for human health. This is done by studying the metabolic pathways that regulate plant nutrient content.

A key element in the Ómicas strategy involves connecting high-throughput phenotypic analysis of plant traits such as morphology, physiology, and behavior with their genetic makeup and the conditions imposed by the surrounding environment. This approach has revolutionized plant breeding by rapidly identifying desirable traits, such as drought tolerance or disease resistance, and developing crops better suited to specific environmental conditions.

In this book, we present several findings associated with the automatic phenotyping of sugarcane and rice crops, from morphological down to molecular traits, along with a few contributions to soil microbiomics and to the development of valuable tools to improve agricultural practices and ultimately ensure food security and human health in the future.

Andres Jaramillo-Botero Carlos Alberto Arango Mambuscay Jaime Aguilar-Zambrano

We want to thank all the contributing authors, the reviewers, Mr. Michael Hernández, Miss Leidi Rojas, and the entire Ómicas alliance team for their effort in producing the results published in this book. We would also like to acknowledge the support provided by the Colombian Scientific Ecosystem, The World Bank, the Colombian Ministry of Science, Technology and Innovation, the Colombian Ministry of Education, the Colombian Ministry of Industry and Tourism, and ICETEX, under GRANT ID: FP44842-217-2018.

This book contains part of the research results on omics sciences, in particular phenomics, of the Ómicas research program of Colombia Científica. The Ómicas program is a research and innovation project led by the Pontificia Universidad Javeriana-Cali with 17 partner institutions including Colombian and world universities, agricultural research centers, and companies in the technological production sector.

The Ómicas program is dedicated to advancing scientific and technological research in two areas of high social impact: food security and sustainable production, in alignment with several UN Sustainable Development Goals, particularly Goal 2: Zero Hunger. The program focuses on research and development in the field of plant omics sciences including genomics, epigenomics, transcriptomics, metabolomics, and phenomics of two vital crops: sugar cane and rice. In addition, the program is involved in developing nanosensors for detecting and quantifying metabolites and contaminants and applying computer science to the in-silico study of natural systems. These cutting-edge technologies are essential to addressing critical challenges in agriculture and ensuring access to safe, healthy, and nutritious food for all.

This research book presents nine articles that have been carefully selected from a pool of 42 proposals that were received in response to an initial call for abstracts. These 42 proposals were evaluated by qualified peers, who selected 38 for further consideration. Of the 38 approved abstracts, 25 complete articles were received, which underwent further evaluation by two evaluators. Finally, 18 articles were approved by the evaluators, and from these, the editorial committee selected the nine best articles to be included in this book on research results in Omic Sciences as follows:

The article Assessment of Morphological and Physiological Characters for Phenotyping of Three Varieties of Sugarcane (Saccharum Officinarum: Poaceae) aimed to evaluate the phenotypic characteristics of three varieties of sugarcane subjected to extreme water deficit conditions, which are expected to occur due to the impact of climate change. The study utilized photoacoustic techniques to evaluate the photosynthetic activity of the sugarcane varieties. The results of the study showed that one of the sugarcane varieties, CC-9338955, exhibited a different behavior in the rate of oxygen evolution by 5%, while the other two varieties were in ranges of around three and four percent.

The article Graph Subspace Fusion from Super-Pixels for Biomass Estimation in Rice Crops uses graph methods to merge multi-spectrum data to extract different crop characteristics in order to estimate above-ground biomass dynamics (AGBD). The article proposes a graph-based subspace fusion to extract features for biomass estimation using aerial multispectral imaging. In the work, a segmentation method is used, a reference node vector is used, and a learning task is carried out using Graph Signal Processing. The method presented is superior in performance to other traditional ones.

The article A Colorimetric Sensor for Detection of Aluminum (III) Using Gold Nanoparticles presents an investigation of the use of the optical properties of nanoparticles for the detection of the presence of Al ³+, which is an ion that alters the productivity of crops and that is present in acid soils.

The article Optimization of Irrigation in CL-86 Maize Production Using Data Mining and Machine Learning presents a method to optimize irrigation conditions in maize crops with the use of information acquisition and processing technology. The method monitors 47 soil and climate variables that influence irrigation processes.

The article Geometrical-Probabilistic Approach to Protein Secondary Structure presents a probabilistic geometric method to identify the secondary structure of proteins. The method is based on the curvature and torsion of the backbone of proteins. Probability distribution functions for the alpha helices, beta sheets, and coils as functions of the curvature and torsion are generated from an initial pool of 186 proteins. The method is tested against a diversity of proteins, obtaining excellent results for alpha helices and acceptable results for beta sheets and coils.

The article Photoacoustic Monitoring of Gros Michel Banana Seedlings Infected with Fusarium Oxysporum F. SP Cubense Race 1 presents a photoacoustic measurement application for the determination of oxygen evolution in banana plants that are affected by Fusarium oxysporum in the seedlings in different states of severity. Phenomic characteristics such as the number of leaves, height, leaf area, and others are analyzed to make comparisons. Differences were identified in the analysis of