meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing

1. MASTER SEMINAR
ON
GENOMICS AND ITS APPLICATION IN CROP
IMPROVEMENT
DATE-24/03/2018
SPEAKER
KHEMLATA THAKUR
M.Sc. (Ag.) Previous
Dept. of Genetics & Plant Breeding
CoA, I.G.K.V, Raipur

2. CONTENTS
• Meaning of Genomics
• Types of Genomics
• Classification of Genomics
• Genome sequencing
• Genes to be Mapped
• Genome Mapping in India
• Role of Genomics in Crop Improvement
• Limitations of Genomics

3. WHAT IS GENOMICS?
• Genomics term was given by Thomas Roderick in
1986.
• Genomics = the branch of molecular biology
concerned with the structure, function, evolution and
mapping of genomes.
• Genome = the complete set of genes or genetic
material present in a cell or organism.

4. Genomics is the sub discipline of genetics
devoted to the
 mapping,
 sequencing ,
 and functional analysis of
genome
 The field includes studies of
intra-genomic phenomena
such as heterosis, epistasis,
pleiotropy and other
interactions between loci
and alleles within the genome.

5. GENETICS VS GENOMICS
and variation

6. Main points related to genomics
 It is a computer aided study of structure and function of entire
genome of an organism.
 It deals with mapping and sequencing of genes on the
chromosomes.
 It is a rapid and accurate method of gene mapping. It is more
accurate than recombination mapping and deletion mapping
techniques.
 The genomic techniques are highly powerful, efficient and
effective in solving complex genetic problems.
 Now use of genomic techniques has become indispensable in
plant breeding and genetics.

7. CLASSIFICATION
OF GENOMICS
Eukaryotic
Genomics
Prokaryotic
Genomics

10. GENOME SEQUENCING
 Genome sequencing is figuring out the
order of DNA nucleotides, or bases, in a
genome-the order of A, C, G, and T that
make up an organism's DNA.
 The human genome is made up of over 3
billion of these genetic letters.

11. Why we need to sequence genome ??
• It determines complete genetic information present in
the genome.
• It provides insights on genome organization and
evolution.
• It has opened up exciting areas for functional
genomics.
• It allows to workout the various molecular interactions.
• Information like SNPs have become available.
• It may provide an understanding of
pharmacogenomics.
• Better understanding of human genetic disease .
• Pathogenicity would be better understood.

12. Methods of gene sequencing
1. Maxam- Gilbert sequencing
2. Chain termination method
3. Pyro-sequencing
4. Nanopore sequencing
5. Clone by clone sequencing
6. Shotgun sequencing

13. ACHIEVEMENTS
EVENTS YEAR
• Discussion in scientific community for sequencing genome 1984-1990
• Human genome project proposed 1986
• Human genome project initiated Oct .1,1990
• Haemophilu influenzae genome sequenced 1995
• E.coli genome sequenced 1997
• Yeast (Saccharomyces cerevisiae) genome sequenced 1999
• Worm (Caenorhabditis elegans) genome sequenced 1999
• Arabidopsis thaliana(a weed) genome sequenced 2000
• Human genome working draft published (90% genome
sequenced)
June 26,2001

14. Genome Size and Gene Number
in some crop plants
CROPS GENOME
SIZE(Mb)
GENE
NO.
YEAR REFERENCE
1) Rice (Oryza sativa) 370 40577 2002 Goff, et al.,
2) Corn (Zea mays) 2500 >32000 2009 Schnable, P et al.
3) Sorghum
(Sorghum bicolor )
700 34496 2009 Paterson , A et al
4) Wheat
(Triticum urartu)
392 - 2013 Ling HQ et al
5) Arabidopsis
(Arabidopsis thaliana)
120 27417 2000 -
6) Soybean
(Glycine max)
950 46430 2010 Haung, et al.
7) Pigeon pea
(Cajanus cajan)
833 48680 2011 Varshney , et al,
8)Potato
(Solanum tuberosum)
844 39031 2011 PGS Constorium
9)Flax
(Linum usitatissimum)
686 43384 2012 Wang,et al

15. Gene to be mapped
 Morphological Characters:
It includes highly heritable traits such as shape, size and colour of
leaf, flower ,calyx, corolla, etc. It also includes surface of leaf
and stem (hairiness and smoothness).
 Productivity traits:
Such characters differ from species to species.
 Resistance Traits:
Such characters include resistance to diseases, insects, drought,
soil salinity, soil alkalinity, soil acidity, heat, frost, water logging, cold, etc.
 Quality Traits:
Such traits include nutritional quality, market quality and keeping quality.
 Agronomic Traits:
Such traits include earliness, plant height, plant type, etc.
 Special Characters:
Such characters include genes controlling male sterility, self
incompatibility, photo and thermo-insensitivity, toxic
substances, apomixes, adaptation, etc.

16. Conventional breeding to molecular
breeding
through Genomic research ?
 Through conventional breeding, selection for crop
improvement is carried out on phenotypic character, which is
the result of genotypic and environmental effects.
 The difficulties of phenotype based selection can be
overcome by direct selection for genotype using DNA
markers that co-segregate with the genes of interest.
 Many potential genes that confer resistance have been
mapped in economical crops like rice.

17. Contd…..
 In conventional breeding normally options of presence of genes can
be identified, when expression where comes during adverse
condition. By the use of genomic research now we can easily identify
the presence or absence of gene in early stage.
 By the use of molecular markers exact location of particular gene on
chromosome can easily be identified.
 Presence of all of the important genes and related markers will be
very much helpful to identified and development of new cultivars as
we desire - Varietal identification.
 Insertion and deletions are desirable or undesirable, easily be
possible to identify with the sequencing of genome.

20. Genome Mapping in India:
• In India, the functional genome research projects are looked after
by the Depart of Biotechnology [DBT] and ICAR.
• The DBT has initiated such work on several crops such as rice,
wheat, maize, chick pea, banana, tomato, Brassica, etc.
• The ICAR has created genome mapping facilities for rice at
NRC-PB, IARI, New Delhi.
• In India, the genome mapping work is carried out at the following
centres.
i. National Research Centre for Plant Biotechnology, IARI, New
Delhi.
ii. International Centre for Genetic Engineering and
Biotechnology, New Delhi.
iii. Jawahar Lal Nehru University, New Delhi.
iv. National Botanical Research Institute, Lucknow.

21. Application of Genomics in Crop
Improvement
•Genome size
•Gene number
•Gene mapping
•Gene sequencing
•Evolution of crop plants
•Gene cloning
•Identification of DNA markers
•Marker assisted selection
•Transgenic breeding
•Construction of linkage maps
•QTL mapping
It is useful
and
provides
information
about

22. Implementation of genomics in
different crops

27. Case study

28. results
• An indica variety with small grain size was crossed to a
japonica variety with large grain size to construct a set of
recombinant inbred lines (RILs) which was used to identify
quantitative trait loci (QTLs) controlling eight grain quality
traits.
• Based on a linkage map of 185 SSR markers, a total of 16
QTLs were mapped on six chromosomes.
• A pleiotropic main effect QTL (M-QTL) flanked by RM3204
and RM16 on chromosome 3 influences the grain length (GL),
length width ratio (LWR) and head rice ratio (HRR), explaining
the phenotypic variation of 46.0, 36.1 and 29.7%, respectively.
• A total of 18 epistatic QTLs were identified for all the traits ,
distributed on all the chromosomes except chromosome 10.

29. GENOMICS STATUS at RRL,IGKV
• Almost all the facilities are available for genomics
• work on structural genomics, functional genomics, are
carried on in RRL
• All kind of markers are available in RRL like SSR. RAPD
etc. For selection, pyramiding .
• Gene mapping ,gene sequencing is done in various crops such
as vegetables, oilseeds basically in rice.
• Advance euipment’s present in RRL are PCR machine, gel
electrophoresis.
• ion torrent machine for gene sequencing
• Availabilty of Taqman based SNP Genotyping.

30. LIMITATIONS
1. Expensive Technique
2. High technical skill
3. Laborious work
4. Limited genes Available
5. Lack of proper markers

31. CONCLUSION
.
• Marker technology has rapidly exerted influence in plant
breeding due to advances in genomics.
• Functional markers have contributed to diagnostics technology
that enable identification of molecules or sequences that
contribute or participate during plant response to various
stresses.
• This has enabled designing of better crop/plant varieties.
• The future of food security depends on availability of funding
to improve agricultural practises for millions of people in
developing countries who depend on it as a source of income
and to ensure the worlds poor are foods secure.

32. THANK
YOU