Plant genomes hold the key to current global issues such as the future of food security and

mitigating climate change. The cutting edge tools in Genomics, Bioinformatics & Systems
Biology to uncover the mechanisms that enable plants to develop, grow, adapt and evolve to
their environment.
There are four main interconnected areas of Plant Genomic Research:
 Plant Developmental Genetics/Genomics
 Plant Systems Biology/Gene Regulatory Networks
 Plant Evolutionary Genomics/Crop Domestication
 Plant Resilience/Response to Environment

The Role of Genomics in Agriculture

The success of transgenic crops has erased the last vestiges of doubt about the value of
agricultural biotechnology and triggered large-scale investments in plant genomics. The term
genomics has a rapidly evolving definition. Genomics is a science that’s defined by technology.
The first genomics technology that was practiced on a large scale was sequencing the 59 ends of
cDNAs, to produce expressed sequence tags (ESTs). ESTs provide a cost-effective and rapid
approach to describing the collection of genes that define an organism. EST sequencing remains
the method of choice for genome-level surveys of eukaryotic organisms. DNA sequence
information unites biology. Determination of an EST sequence permits an immediate search of
sequence databases for similarity to sequences with known functions from any organism. The
information content of an EST database primarily is derived from links with other databases.
Discovery of function in one organism provides insight to related sequences in all organisms.
Inexpensive, fast DNA sequencing has replaced expensive, slow experimentation. This makes
sequencing attractive to companies that develop gene-based products, such as transgenic crops.
All of the large genetic supply organizations have in-house genomics programs or access to
proprietary databases. Creating an EST database of our major crops should be the top priority for
agricultural plant genomics. In contrast, complete genome sequencing is currently only practical
for microbes with small genomes, with the exception of a few large, international efforts to
sequence the yeast, human, nematode, fruit fly, and mouse-ear cress genomes. The sequence of
the latter, also known as Arabidopsis thaliana, will be invaluable for both science and the
development of agricultural products. Contributing to the timely completion of the Arabidopsis
sequencing project should be the second-highest priority for agricultural plant genomics.
Genomics will accelerate the application of gene technology to agriculture. As previously
described, this technology will enhance food security, by increasing productivity, and food
safety, by eliminating mycotoxins. There is a third benefit, derived from the first two: increased
wealth. By accelerating the application of technology, genomics significantly increases the value
of seeds and agricultural products. This increase adds much wealth to the customers, company
owners, employees, and citizens of the nations in which genetic supply companies operate, and
to both producing and importing nations whose food costs consequently are decreased.
Genomics is a field of science that focuses on the study of an organism’s entire set of genetic
material, called its genome.
This includes studying the structure, function, and interactions between all of the genes and other
components that make up the genome. The genome of an organism is made up of DNA, which
contains the instructions for how that organism develops, functions, and interacts with the world
around it.
Categories of Genomics
 Two broad categories of genomic studies are – structural genomics and functional genomics.
 Structural genomics is the field of genomics that deals with structures of genome sequences.
Understanding the genome structure involves constructing genome maps, sequencing genes,
annotating gene features, and comparing genome structures.
 Functional genomics deals with the study of gene expression and the function of genes in a
genome. It involves studying gene functions at the whole genome level using high-throughput
methods.
In addition to structural and functional genomics, there are other subfields of genomics,
including:
 Epigenomics involves the study of epigenetic modifications or epigenome, which refers to the
collection of chemical compounds that attach to DNA and influence its activity. The epigenome
plays an important role in determining the differences between various cell types in the body.
Epigenomic modifications include DNA methylation and histone modification.

 Metagenomics involves the study of genetic material from entire biological communities rather
than just individual organisms. It is generally applied to microorganisms. Metagenomics can be
used to study the diversity and function of microbial communities in diverse environments,
such as the human gut, soil, or ocean.

 Pharmacogenomics is the subfield of genomics that uses an individual’s genetic information to

study and customize the choice and dosage of drugs in medical treatment. It can be used to
predict drug response or toxicity and to develop a more personalized approach to prescribing
drugs.

 Comparative genomics involves the comparison of genomes from different species that can
provide insights into evolutionary relationships, functional elements, and genetic variations
among species. It uses various tools that help to identify and understand the similarities and
differences in the genomes of various species.

Methods in Structural Genomics

Genome mapping
 Genome mapping is a crucial process in structural genomics which involves the identification
of the locations of genes, mutations, or traits on a chromosome.
 There are different types of genome maps, including genetic linkage maps, physical maps, and
cytologic maps.
 Genetic linkage maps, also referred to as genetic maps, are low-resolution maps that use
inheritance patterns to determine the relative positions of genetic markers on a chromosome.
 Physical maps are high-resolution maps that identify the locations of recognizable landmarks
on a genomic DNA regardless of inheritance patterns.
 Cytologic maps, also known as chromosome maps, describe the banding patterns visible on
stained chromosomes, which can be directly observed under a microscope. These visually
distinct light and dark bands serve as markers on the chromosomes.
 Genome sequencing
 The most detailed genome map is obtained through genome sequencing, which determines the
complete DNA sequence of the genome.
 A widely used DNA sequencing method is Sanger sequencing. It uses fluorescently labeled
dideoxy nucleotides to terminate DNA chains of varying lengths. The resulting fragments are
separated by electrophoresis, and the sequence is determined by reading the banding pattern in
the gel. Base calling is used to assign bases for each peak in a chromatogram.
 Whole genome sequencing can be done using two main methods: shotgun sequencing and
hierarchical sequencing.
 In shotgun sequencing, DNA clones are randomly sequenced from both ends. This generates a
large number of DNA fragments, which are then assembled by a computer program to create a
complete genome sequence.
 The hierarchical method involves mapping chromosomes using physical mapping techniques.
Longer fragments of genomic DNA are cloned into a bacterial vector with high capacity. The
physical map helps determine the locations and order of the cloned fragments on the
chromosome.

S
anger Sequencing
 Genome sequence assembly
 Genome assembly is the process of reconstructing a complete genome sequence from a large
number of short DNA fragments called reads.
 DNA sequencing reactions produce short sequence reads derived from DNA clones. To
reconstruct the complete genome, these short fragments need to be joined together while
removing any overlapping regions.
 The first step in the genome assembly process is base calling which derives base calls and
assigns quality scores to these base calls. Base calling is used to determine the sequence of
nucleotides at every position in the DNA fragments. Quality scores are assigned to each base
call, which represents the confidence or accuracy of the base call.
 The next step is to assemble the individual sequence reads into contiguous sequences, known as
contigs. This involves identifying overlaps between the different fragments, determining their
relative order, and then deriving a consensus sequence for each contig.
 There are several commonly used programs for processing raw sequencing data and assembling
contigs, including Phred, Phrap, TIGR Assembler, and ARACHNE.
Genome annotation
 After the assembly of the genome sequence, it needs to be analyzed to identify and annotate
useful biological features. The process of analyzing and interpreting genome sequences using
computational methods is called genome annotation.
 Genome annotation process involves two main steps: gene prediction and functional
assignment.
 In gene prediction, computational programs are used to predict the locations and structures of
genes within the genome.
 The next step is to assign functions to the predicted genes. This is done through homology
searching, primarily using BLAST.
 The resulting annotations are deposited into public databases like GenBank, making them
accessible to the scientific community for further analysis and research.

Methods in Functional Genomics

Genetic interaction mapping
 Genetic interaction mapping is a technique used to study the functional relationships between
genes. It refers to the study of how multiple genes interact with each other to influence specific
phenotypic traits.
 This approach involves perturbing genes in pairwise combinations, such as through knockout,
knockdown, or overexpression, to understand how one gene influences the phenotype of
another.
 Epistasis is one such genetic interaction. It is a form of interaction between non-allelic genes
that occurs when the effect of one gene is masked by another gene.
 There are numerous computational tools available for detecting gene-gene interactions. Some
examples include BEAM (Bayesian Epistasis Association Mapping), TEAM (Tree-Based
Epistasis Association Mapping), BOOST (Boolean Operation-based Screening and Testing),
and TS-GSIS (Two Stage-Grouped Sure Independence Screening).
 Genetic interaction mapping is useful in discovering new gene functions and organizing gene
products into functional complexes and pathways in a hierarchical manner.
 Microarray technology
 Microarray-based approaches are widely used in genomics research for global gene expression
profiling.
 A microarray is a chip that contains a high-density array of immobilized DNA oligomers or
complementary DNAs (cDNAs). Each oligomer serves as a probe that can bind to a specific
complementary cDNA molecule.
 In a microarray experiment, the labeled cDNA molecules are fluorescently or radioactively
labeled and allowed to hybridize with the oligo probes on the chip. The amount of fluorescence
or radiolabels at each spot on the microarray indicates the level of mRNA abundance in the
cell.
 This technology enables the rapid and systematic analysis of gene expression patterns and
facilitates the discovery of novel gene functions and regulatory mechanisms.
 Microarrays have various applications in functional genomics. They are used for comparing
gene expression patterns between normal and diseased tissues, identifying single nucleotide
polymorphisms (SNPs) in genes, and detecting alterations in chromosomal copy numbers.

DNA-Microarray
 SAGE
 SAGE (Serial Analysis of Gene Expression) is a high-throughput, sequence-based method used
for analyzing gene expression profiles. It provides information about mRNA expression levels
in a cell.
 Unlike microarray technology, which relies on hybridization, SAGE directly sequences RNA
molecules to provide a global analysis of gene expression.
 In SAGE, short oligonucleotide sequence tags called SAGE tags are isolated from individual
mRNAs and used as unique markers for gene transcripts.
 These tags are concatenated, cloned, and sequenced. The analysis of gene expression is
performed computationally in a serial manner. The frequency of each gene tag indicates the
level of gene expression.
 SAGE also has some limitations. The sequencing step is costly and time-consuming, and
determining the number of tags to be sequenced for good coverage of the entire transcriptome
can be challenging.

Applications of Genomics
 Genomics helps in the diagnosis and classification of diseases by identifying specific genetic
changes. Genomics studies the genetic basis of diseases, identifying variations linked to
specific conditions, predicting disease risk, and developing targeted treatments.
 Another application of genomics is pharmacogenomics which studies the impact of genes on an
individual’s response to drugs. It analyzes genetic variations to determine the most effective
and safe medications for personalized medicine.
 Comparative genomics compares the genomes of different species in order to identify
similarities, differences, and evolutionary relationships. This helps in understanding the genetic
basis of traits, evolutionary processes, and the diversity of life on Earth.
 Genomics also plays a crucial role in agriculture by enhancing crop and livestock breeding,
improving disease resistance, and increasing agricultural productivity. It helps in the
identification of genes related to desired traits and in developing superior crop varieties and
livestock breeds.
 Genomic analysis also has applications in forensic and criminal investigations. DNA samples
found at crime scenes can provide valuable information, help identify suspects and determine
relationships between individuals.