Introduction To Genetics

Introduction to Genetics
Agus Budi Setiawan, S.P., M.Sc., Ph.D.

Genetics and Plant Breeding Lab, Department of Agronomy, Faculty of Agriculture, UGM
The Terms and Conditions
SK Rector No: 1666/UN1.P.I/SK/HUKOR/2016
Course outcomes
Able to explain the history and basic concept of genetics,
CPMK 1 cell division, structure and cell cycle, and chromosomes
Able to point out mendelian genetics, Mendel’s law I

CPMK 2 and II and ratio of Mendelian inheritance
Able to explain gene-linked, crossing over,

CPMK 3 gametes development, gene configuration in chromosomes
Able to explain the chemistry of inheritance, central

CPMK 4 dogma biology, DNA structures, and gene regulations
1st Tri-semester
Lecture subjects
8 February 15 February 22 February
• The overview of • Cellular • Cell division

genetics: reproduction: and cell cycle
history and Cells and (mitosis &
basic concept Chromosomes meiosis),
of genetics. (organization chromosome
and function) structures.
1st Tri-semester
Lecture subjects
1 March 8 March 15 March 22 March
• Mendelism: • Extension of • Non- • Non-

The Basic Mendelian Mendelian Mendelian
Principles of Inheritance: Inheritance: Inheritance:
Inheritance Inheritance Maternal Extranuclear
• Law of Patterns of Effect and Inheritance
Segregation Single Epigenetic
• Law of Genes and Inheritance
Independent Gene
Assortment Interactions
How to join our class?
1 2
Login to elok using your SSO account

Choose Genetika Pertanian. Password: genetika2021
3
All subject materials , Quiz, Mid-Term and Final Exam of
appropriate class are available there
The chapters
The great milestones in genetics
DNA as genetic material
Genetics and evolution
Level of genetics analysis
The application of genetics in agriculture

Milestones of Genetics and Plant Breeding
The milestones of Genetics
v The genetics concept is firstly established by Gregor
Mendel, who discovered how traits are inherited.
• Gregor Mendel postulated the
existence of particulate
factors, now called genes, to
explain how traits are inherited.
• Alleles, the alternate forms of
genes, account for heritable
differences among individuals.
v The molecular basis of heredity was revealed when James
Watson and Francis Crick elucidated the structure of
DNA.
• James Watson and Francis Crick
elucidated the structure of DNA, a
macromolecule composed of two
complementary chains of
nucleotides.
• DNA is the hereditary material in all
life forms except some types of
viruses, in which RNA is the
hereditary material.
v The Human and plant genome project is currently
engaged in the detailed analysis of human and plant
DNA.
• The Human and plant
genome Project determined
the sequence of
nucleotides in the DNA of
the human and plant
genome.
• Sequencing the DNA of a
genome provides the data to
identify and catalogue all the
genes of an organism.
Collins et al. 2003. Nature 422: 835-847
Piquerez et al. 2014. Front. Plant Sci. 5 (671)
Arabidopsis is a
model in plant
research and
completely
sequenced
Sivasubramanian et al. 2015 . DOI 10.1007/978-81-322-2283-5_1 Siroky et al. 2003. Chromosoma 112(3):116-23
Plant genomes compose of numerous nucleotide sequences,
particularly repetitive sequences.
Teh et al. (2017)

Utilization of plant genome sequence
• Development of Marker Assisted Selection (MAS) in molecular
genetics and plant breeding.
• Genetic mapping via development of DNA/Protein sequence
probes through physically mapped-FISH and Immunostaining in
molecular cytogenetics.
71E = a positive control for all three sex types.
W11 is a male/hermaphrodite specific marker
The Sequencing of
papaya X and Yh
chromosomes
discovered the
male specific male-specific DNA marker PMSM1 and PMSM2
markers
Wang et al. 2012. PNAS. 194 (34): 13710-13715 Liao et al. 2017. Euphytica. 213: 53
Z. Kubat, E. Kejnovsky, B. Vyskot & R. Hobza
(Institute of Biophysics, Brno, Czech Republic)
G. Mirzaghaderi (University of Kurdistan, Iran)
Development of centromeric probe for
Cmcent
Clear identifying of plant centromeres CmSat162
10 µm
DAPI Cmcent CmSat162 Merged
Setiawan et al. (2020)

https://doi.org/10.1371/j
ournal.pone.0227578
Precise karyotyping of Cucumber Chromosomes
45S rDNA 5S rDNA Subtelomeric-Type 1
Clear identification of homologous chromosomes
https://doi.org/10.11352/scr.21.81 Wibowo et al. (2018)

Cytological Distinctions Between Timun Suri and
Cucumber confirmed by 45S rDNA
Cucumber 45S rDNA
Molecular
cytogenetics
Melon evidences for
distinguishing
timun suri and
cucumber
Timun suri
Setiawan et al. (2020)
http://doi.org/10.17
503/agrivita.v42i3.
2142
DNA as the Genetic Material
• Central dogma flows from DNA to RNA to protein.
• When DNA replicates, each strand of a duplex molecule
serves as the template for the synthesis of a complementary
strand
DNA as the Genetic
Material
• When genetic information is
expressed, one strand of a
gene’s DNA duplex is used as
a template for the synthesis of
a complementary strand of
RNA.
• For most genes, RNA
synthesis (transcription)
generates a molecule (the
RNA transcript) that becomes
a messenger RNA (mRNA).
• Coded information in an
mRNA is translated into a
sequence of amino acids in a
polypeptide.
• Mutations can alter the DNA

sequence of a gene.
• The genetic variability
created by mutation is the
basis for biological
evolution.
The mutation of Vrs1 gene in Barley
mutagens
Vrs1 Int-d hex-v
Komatsuda et al. 2016. PNAS. 104 (4): 1424-1429

Insertion of LTR-Retrotransposon regulated the blood orange phenotype
Grandbastien (2015)
Genetics and Evolutions
v Genetics has much to
contribute to the scientific
study of evolution.
• Evolution depends on the
occurrence, transmission,
and spread of mutant
genes in groups of
organisms.
• DNA sequence data
provide a way of studying
the historical process of
evolution.
Sebastian et al. 2010. PNAS. 107 (32): 14269-14273
Comparative analysis of the melon and watermelon genetic maps with
the cucumber sequence map
Huang et al. (2009)

The collinearity of melon with cucumber chromosomes indicating the speciation event of each
cucumber chromosomes resulted from a fusion of two ancestral chromosomes
Molecular cytogenetic evidence of genome evolution
in melon and cucumber
Melon
10 µm
Cucumber
10 µm
Setiawan et al. (2020).Cytogenet Genom Res. 160: 554-556

Levels of Genetic Analysis
v Geneticists approach their science from different points
of view - from that of a gene, a DNA molecule, or a
population of organisms.
• In classical genetic analysis, genes are studied by following the
inheritance of traits in crosses between different strains of an
organism.
• In molecular genetic analysis, genes are studied by isolating,
sequencing, and manipulating DNA and by examining the
products of gene expression.
• In population genetic analysis, genes are studied by assessing
the variability among individuals in a group of organisms.
Application of plant genetics and molecular for
trait dissection and crop improvement Varshney et al. (2018)
Applications of genetics for the better of
agriculture
• Genetics is relevant in
many venues outside
the research laboratory.
• Discoveries in genetics
are changing
procedures and
practices in agriculture
Che and Zhang. 2019. Curr. Opi. Plant Bio. 47: 38-46
The role of genetics in crop improvement
Two-rowed Six-rowed
The domestication
and selection
through genetic
approaches
Wild & significantly
increased crop yield.
Cultivar Cultivar
Komatsuda et al. 2016. PNAS. 104 (4): 1424-1429

The GM Crop and Genome Editing
IR: Insect Resistant
HT: Herbicide Tolerant
DT: Drought Tolerant
VR: Virus Resistant
Byrne (2014)
Zhang et al. (2018)

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Introduction to Genetics

Agus Budi Setiawan, S.P., M.Sc., Ph.D.

Able to point out mendelian genetics, Mendel’s law I

Able to explain gene-linked, crossing over,

Able to explain the chemistry of inheritance, central

8 February 15 February 22 February

• The overview of • Cellular • Cell division

1 March 8 March 15 March 22 March

• Mendelism: • Extension of • Non- • Non-

Login to elok using your SSO account

DNA as genetic material

Genetics and evolution

Level of genetics analysis

The application of genetics in agriculture

Teh et al. (2017)

DAPI Cmcent CmSat162 Merged

Setiawan et al. (2020)

Clear identification of homologous chromosomes

https://doi.org/10.11352/scr.21.81 Wibowo et al. (2018)

Setiawan et al. (2020)

• Mutations can alter the DNA

Vrs1 Int-d hex-v

Komatsuda et al. 2016. PNAS. 104 (4): 1424-1429

Huang et al. (2009)

Setiawan et al. (2020).Cytogenet Genom Res. 160: 554-556

Komatsuda et al. 2016. PNAS. 104 (4): 1424-1429

Zhang et al. (2018)

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