GENOMICS

AND
CROP
IMPROVEMENT
 Genomics and crop improvement
 Genome contains total genetic information
carried by a single set of chromosomes in
a haploid nucleus
 It is the unit of information transmission
(DNA replication) whereas genes in an unit
of expression
 Genomics is the study of genes and their
role in the structure, growth and
development, quality, health and diseases
of plants
 Application of Genomics
 Gene structure
 Gene identification and cloning
 Gene prediction/ discovery
 Genetic mapping and locating genes
 Genome projects
 Genomic database
 Genome manipulation (Mol. Biology)
 QTLs
 Molecular markers and MAS
 Diagnostics on the basis of transcription to RNA
and translation to protein
 Study of Genomics
 Karyotype analysis/ chromosome profile
 Molecular cytogenetics
 Molecular dissection
 DNA studies & DNA sequencing
 Gene discovery
 Search for new genes
 Exon Prediction
 Comparative genomics & orthologous loci
 Gene expression and traits
 Genome projects

Genomic library: DNA library in which the

cloned DNA is from a genomic DNA of the
plant
Application of genomics (Contd)

 Comparative genomics
 Gene banks and chromosome stocks
 Expression (mRNA) profiles and
responses and interactions
 Data bases and Networking
 Genome projects
 Crop improvement
 Plant Genomic Strategies
 Diversity Genomics
 Applied Genomics
 Genome Vision
 Structural Genomics
 Comparative Genomics
 Functional Genomics
 Nutritional Genomics
 Computational Genomics
 Integrative Bioinformatics plus K mgt
 Cell cycle / Mitosis
 Life cycle of a cell marked by cell
division. The four phases are:
 G1 (Gap 1)
 S (Synthesis) DNA replication’
 G2 (Gap 2)
 M (Mitotic phase) Chromosome
separation
 Replication in a short time with precision
 Somatic cells
WALTHER FLEMMING (1882)

Describes “
MITOSIS”
DESCRIBES STAGES OF MEIOSIS
 Crossing Over

 Crossing over (variation) may occur

between nonsister chromatids at the
chiasmata.
 Crossing over: segments of nonsister
chromatids break and reattach to the
other chromatid.
 Chiasmata (chiasma) are the sites of
crossing over.
 Crossing Over - variation
nonsister chromatids Tetrad

chiasmata: site variation

of crossing over
 Chromosome structure
 Cell cycle (replication)
 Interphase cells – DNA – Protein complex
 Euchromatin and Heterochromatin
 Euchromatin is the chromatin region relatively
open, less condensed where gene expression
occurs
 Heterochromatin are chromatin regions that are
always highly condensed and there is little gene
expression in these regions. Heterochromatin
takes stain during metaphase
 Heterochromatin is either constitutive or
facultative
 Constitutive heterochromatin is the specific
genome region often containing short repeated
sequences
 Facultative heterochromatin is the entire
chromosome that are transcriptionally inactivaed
 Cytogenetics - application
 Genome manipulation
 Polyploidy (Amplification)
 Chromosome number changes
 Chromosome structure alterations
 Alien addition/ Transfer of chromosomes
 Alien substitution of chromosomes
 Alien gene transfer
 Genome amplification: Intrachromosomal or
extrachromosomal production of many DNA
copies from a certain region of DNA/ Chromosome
occur spontaneously
 Chromosome engineering 1960s
 Organelle Genomes
(specialized functions)
 Mitochondria
 Occurs in large numbers in the cytoplasm of
eukaryotic cells
 Double membrane bound structure
 Semi autonomous organelle containing its own
DNA (mt) and Ribosomes
 Reproduces by binary fission
 Chloroplast-semi autonomous
 Chloroplast DNA (Cp DNA)
 Responds to nuclear signals
 Inter genomic interactions
Why CG
 Comparative genomics
Characters

Identical Sharing the corresponding

characters

Similar Sharing identities

Analogous Homologous

Similar due to convergence Similar due to common ancestors

Orthologous Paralogous

Homologous due to Homologous with

conserved function divergent functions
 What to compare
PARALOGUES
Genes within the same genome
that share an ancient gene
performing diverse biological
functions
ORTHOLOGUES
Genes that share the same
ancestral gene performing same
biological function in different
species but have diverged in
sequence due to selective
evolution
 Diversity genomics
 Sequence polymorphism
 Heritable phenotypic differences
 Genetic diversity
 Novel molecular markers/traits
 Linkage disequilibrium in natural and
domesticated crop plants
 Selection sweeps in genomics regions
 Introgression scales
 Mechanisms of crop diversity
Functional Genomics
 Functional Genomics
Genome sequence

Gene identification

Gene expression Gene function

cDNA Protein Co-expression Protein modification
expression expression Structure interaction

Gene trapping
Mutagenesis

Genetics manipulation
SY ST EMS VIEW OF C EN TRAL
DOGMA
 CE NTRAL DOGM A OF
MO LECUL AR BI OLOGY
GENE S TRU CTU RE
GE NE EX PR ESS IO N
GE NE EX PR ESS IO N
 MOLECULES PARTICIPATING IN
INFORMATION FLOW AND THE
FUNCTIONAL SITES
MOL EC UL PRO CE SSI NG FUN CT IO NAL SI TE S INT ER AC TIN G
E MOL EC UL ES
DNA REP LI CAT IO N REP LI CA TIO N O RI GIN ORI GI N
TRA NS CRI PT ION PRO MO TO R REC OG NI TIO N
COM PL EX
ENH AN CE R
OPE RA TO R RNA P OL YME RAS E
OTH ER P ROK ARY OT IC TRA NS CR IPT ION
REG UL AT ORS FAC TO R
REP RE SS OR etc
RNA POS T- SPL IC E SIT E SPL IC EO SOM E
TRA NS CRI PT ION
AL PR OCE SS ING TRA NS LA TIO N RIB OS OM E
TRA NS LAT IO N INI TI AT ION SI TE
CONT.. MOLEC ULES PARTI CIPAT ING IN
INFO RMAT ION FL OW AN D TH E
FUNC TION AL SIT ES
MOL EC UL PRO CE SS ING FUN CT ION AL SI TE S INT ER ACT ING
E MOL EC ULE S

PRO TE IN POS T- CLE AV AGE S ITE PRO TE ASE

TRA NS LA TIO NA PHO SP HOR YL ATI ON PRO TE IN
L P RO CE SSI NG AND O THE R KIN AS E e tc
MOD IF ICA TI ON SI TES
ATP B IND IN G S IT ES
PRO TE IN SIG NA L S EQ UEN CE , SIG NA L
SOR TI NG LOC AL IZA TI ON REC OG NIT ION
SIG NA LS PAR TI CLE
PRO TE IN DNA B IND IN G S IT ES DNA
FUN CT IO N LIG AN D B IN DIN G LIG AN DS
SIT ES MAN Y
CAT AL YTI C SIT ES DIF FE REN T
MOL EC ULE S
 Functional Genomics
 Ways of identifying gene function and assigning
functions to genes of unknown functions

 Gene family
 Group of similar or identical genes usually on the same
chromosome, arising by gene duplication some of them
work and some of them are switched off or silenced
(pseudo genes)

 Gene(Genome) amplification
 More or less specific production of multiple copies

 Gene conversion
 Process in which one member of a gene family acts as a
blue print for the correction of the other - can result in
either suppression of a new mutation or its lateral
spread in the genome
 Genomics – overview of general
functions
 Genome sequence gene
identification gene
expression gene function
 Gene identification – genomic motifs,
comparative genomics, cDNA & ESTs
database, Protein identification
 Gene expression – cDNA expression,
Protein expression
 Gene expression
 Gene activation
 Process in which information in a gene is
used to produce a protein and gene
expression via transcription and
translation to produce protein and hence
phenotype
 Gene-phenotype relationship (functions)
understanding the field plot techniques,
stat.procedures, molecular markers,
information techniques and equipments
 Gene transfer/ genetic engineering
 Chromosome engineering
 Exon
 Exon prediction and Exon trapping
 Exon is the portion of the gene that is
transmitted into the mRNA and is
translated into protein
 Exon trapping is the method used to
isolate exons from new DNA. In exon
trapping, an R fragment from a new
DNA sequence is cloned into a cognate
R site in an intron of a cloned gene
 Expressed sequence tags
 DNA sequences derived by sequencung an
end of a random cDNA clone from a library
of interest. Provides rapid ways of
identifying cDNA of interest based on their
sequence EST is an exon specific
sequence.50-500 bp from a cDNA. It
represents a gene. Large sets of ESTs
opens the door for studying gene
expression on a large scale. ESTs represent
tags of expression for a given cDNA library.
(Rastogi et al ., 2004)
 Size of mRNA
 Gene size: Gene is sequence of chromosomal
DNA required for production of functional RNA
molecule or functional protein. Range in size from
1.5Kb (globin gene) to 2000 Kb (muscular
distrophy gene)
 RNA: It is single stranded. RNAs are mRNA, tRNA,
rRNA
 mRNA is about 1/10th of the size of the gene from
which it is transcribed
 mRNA levels define state of the cells. 5% mRNA,
15% tRNA and 80% rRNA of total RNA. Other
minor RNAs are involved in splicing and telomere
synthesis
mRNA contd….

 mRNA
 mRNA is template for protein synthesis
 assume double helix or single stranded
structure
 does not contain chemically modified bases
 tRNA
 Function in protein synthesis
 Contain chemically modified bases
 Single stranded DNA and RNA
 Adopt random coil structure

 Ribosomes
 Subcellular organelle involved in protein
synthesis
 Made of large and small subunit and rRNA is
integral part of it
 rRNA is single stranded and contains chemical
 Markers are many..
 RFLP – Restriction Fragment Length
polymorphism
 RAPD – Randomly Amplified Polymorphic DNA
 VNTRs – Variable Number Tandem Repeats
(sat.DNA, omni sat, microsat)
 SSR – Single Sequence Repeats or
Microsatellites
 DAF – DNA Amplified Finger Printing
 AP-PCR – Arbitarily primed PCR
 STS – Sequence Tagged Site
 SCAR – Sequence Characterized Amplified
Regions
 CAPs – Cleaved Amplified Polymorphic Sequence

TYPES OF MARKERS IN GENETICS
 MAPS are different kinds
 Chromosome/ cytogenetic map in terms of
Chromosome Banding
 Genetic mapping/ linkage maps
 cDNA map showing locations of expressed DNA
regions (exons) on the chromosome map
 Cosmid contig map showing the order of
overlapping DNA fragments
 Macro restriction map – order of distance
between enzyme cutting cleavage site
 Highest restriction physical map showing the
complete elucidation of the DNA sequence of
each chromosome in the genome
 Physical mapping
MOLECULAR MARKERS AND GENETIC
MARKERS
 Quantitative Trait Loci (QTL)
 Linkage of trait (Quantitative) to marker
loci i.e. phenotype for the QT and
genotype for the marker loci are scored
and if there are differences between mean
phenotype among the marker genotype
classes, then presence of QTL linked to the
marker is inferred. The association
between quantitative trait variation and
marker segregation pattern is worked out.
It is quantified linkage disequilibrium to
locate and clone gene responsible for QT.
QTL is locus of DNA segments that carry
more genes coding for an agronomic trait
 DNA Micro array – Recent
Technology
 Measures relative to the number of copies
of a genetic message and thus levels of
gene expression at different stages in
development and in different tissues. It
can even measure poorly expressed genes
 It is referred to as Reverse Northern. In
micro array experiment, (array
hybridization) cDNA are spotted onto a
filter and hybridized with a probe made
from mRNA population. Probes are made
by reverse transcribing mRNA into cDNA
Microarray contd………
 The amount of hybridization to a given

clone represents the amount of mRNA

present to the corresponding gene
 Applications
 Gene expression profiling
 Identifying new targets for functional genomics
 Single nucleotide polymorphism mapping
 Genotyping
 A tool in proteomics to indicate protein

abundance. mRNA and protein levels do not

always correlate in the cells
 Why DNA Microchip
technology?

 DNA microarray gives snapshot of mRNA expression
    in a genome at a particular time
 Can take multiple snapshots to watch changing
    patterns of mRNAs over time, space and in response 

    to stimuli
 E.g.: Developmental stages, Different tissues, 
          Starvation, Disease invasion, etc.

 Can give indirect indication about levels of specific 
Phenotypes and arrays
 Plant Breeding Application
 Gene discovery
 Molecular breeding – get into genes
 Diversity patterns and evaluation
 Molecular fingerprinting
 Marker Assisted/ Aided selection
 Markers and genetic solutions
 Marker development
 Purity testing develop computational models for
biological functions (for traits of interest/ target
traits)
 Manipulate value added traits
 QTLs – pyramiding and interactions
 Transformation and traits
 Biotic and abiotic stresses and diagnosis
GENOME
COMPARISONS

Research Directions
 COMPARITIVE GENOMICS OF TOMATO, POTATO AND
PEPPER
Comparative genomics of
grasses
Rice Genome Utilities
 Proteomics
 PROTEins expressed by genOME is
proteomics (Wilkins, 1995). Genome is
entire set of genes and like that proteome
is inclusive of all proteins produced by a
species. Unlike genome, proteome varies
with time and sample

 Proteomics Application
1. Identifying diseases progression
2. Protein markers for diagnostics
3. Information generated in proteomics is
complementary with the Genomics information
 Bioinformatics
 Bioinformatics is management information
system for molecular biology. It is the
application of information techniques
derived from disciplines such as applied
mathematics, computer science and
statistics to understand and organize the
information associated with the molecules
(molecular biology) and biological
phenomena / functions
 It is the mathematical, statistics and
computing methods that aim to solve
biological problems using DNA and amino
acid sequences and related information
Component inter relationships

Genetics Plant Development

Cytogenetics

Bioinformatic Plant Manipulations

Synthetic approach
Genomics

Crop Improvement
Proteomics