2. Presented by :
Kanak Saxena
Roll No.-234
Guided by:
Dr (smt.) Rajani
Bisen
Advances in Cereal Genomics and its
application in crop improvement
3. CONTENTS
Introduction
Genomics
Need of Genomic research in cereal crops
Laboratories for Cereal Genomic Research in India
Genomics based approaches and techniques
Role of genomics in crop improvement
Achievements in Cereal Genomics
Case Study
Challenges in using genomics for breeding
Conclusion
References
4. (Genomics word was coined by Thomas Roderick in 1986.)
(Study of structure & function of entire genome of a living organism)
(Study of the structure of
entire genome of an organism)
(Study of the function of
entire genome of an organism)
GENOMICS
Structural Genomics Functional Genomics
Comparative Genomics
(Study of the relationship of genome structure and
function across different biological species or strains)
5. 1980 – DNA markers (RFLP)
1983 – Karry Mullis invented the PCR technique, and Several
PCR based markers developed i.e. RAPD, AFLP, SSR, SNP,
CAPS, STS, SCAR, EST, etc..
1986 – Leroy Hood and Lloyd Smith developed the first semi-
automatic DNA sequencer
1990 – Development of Pyrosequencing by Pal Nyren
1990 – The U.S. National Institutes of Health (NIH) begins large-
scale sequencing trials on Mycoplasma , Escherichia coli,
Caenorhabditis elegans, and Saccharomyces cerevisiae
1995 – Craig Venter, Hamilton Smith at The Institute for
Genomic Research (TIGR) publish the first complete genome of a
free-living organism, the bacterium Haemophilus influenzae
1996 – Sequence of saccharomyces cervisiae genome completed.
Nature Review, 2010 & Nature Biotechnology, 2001-2013
6. 1998 – The genome of the 1st multi-cellular organism of the Round worm
(Caenorhabditis elegans) was completed.
1999 – Sequence of first human chromosome (chromosome 22nd)
2000 – The first plant to be completely sequenced is that of the
Arabidopsis thaliana.
2001 – A draft sequence of the human genome is published.
2002 – Rice genome sequencing was completed
2003 – Human genome sequencing was completed
2004 – 454 Life Sciences markets a version of pyrosequencing machine
developed. ‘454 Sequencing’ used in Barley this machine reduced
sequencing costs 6-fold compared to automated Sanger sequencing
methods.
Recently,
2012 – Wheat genome was sequenced – R. Brenchley et al.
2012 –Barley genome was sequenced – RKV et al.
Nature Review, 2010 & Nature Biotechnology, 2001-2013
7. Genome size, structure and genomic resources of major
cereal species
Rajeev K. Varsney et al (2013)
8. CROP BOTANICAL NAME GENOME SIZE
(Mb)
RICE Oriza sativa 400
SORGHUM Sorghum bicolar 1000
MAIZE Zea mays 2500
BARLEY Hordeum vulgare 8000
BREAD
WHEAT
Ttriticum aestivum 16000
ESTIMATED GENOME SIZE OF MAJOR CEREAL CROPS
Rajeev K. Varsney et al (2013) Trends in biotechnology
11. Through conventional breeding, selection for
crop improvement is carried out on phenotypic
character, which is the result of genotypic and
environmental effects but by the use of
molecular markers exact location of particular
gene on chromosome can easily be identified.
Many potential genes that confer resistance
have been mapped in most of the economically
important cereal crops like Rice, Maize, Wheat,
Sorghum and Barley.
QTLs identified and markers linked with the
promising QTLs are useful resource for
genomics assisted breeding. For ex. resistance
to heat tolerance in wheat.
11
12. 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 cereal crops.
Generated set of ESTs serves as a resource of high
quality transcripts for gene discovery and
development of markers associated with abiotic
stress tolerance that will be helpful to facilitate
cereal genomic breeding.
13. Laboratories for genomic research in India
National Research Centre for Plant Biotechnology, IARI, New
Delhi
International Centre for Genetic Engineering & Biotechnology,
New Delhi
Jawaharlal Nehru University , New Delhi
National Institute of Plant Genome Research, New Delhi
ICRISAT and DRR ,Hyderabad
14. International Institutes for Cereal Genomic Research
Genome Institutes/ Countries Involved
Rice Genome
Jointly Mapped By IRRI, USA, China, Japan
Scientist through International Rice Genome
Sequence Project.
Wheat Genome
International Genome Research on Wheat by
Mexico (CIMMYT), UK, USA & Japan
Arabidopsis Genome China, Japan, & USA
17. A holistic approach, where genomics technologies
including molecular markers, trasncriptomics,
metabolomics, proteomics and bioinformatics are
integrated with conventional breeding strategies for
breeding crop plants resistant/ tolerant to biotic and
abiotic stresses or improved for quality and yield.
3 Next generation sequencing (NGS) technologies
Include various novel sequencing technologies for example
454/FLX (Roche Inc.), ABI SOLID (Applied Biosystems),
Solexa (Illumina Inc.) etc. that have surpassed traditional Sanger
sequencing in throughput and in cost-effectiveness for generating
large-scale sequence data.
2 Genomic Assisted Breeding
18. Clone by clone sequencing also called as the directed
sequencing of the BAC contigs.
The chromosomes were mapped
Then split up into sections
A rough map was drawn for each of these sections
Then the sections themselves were split into smaller bits.
Each of these smaller bits would be sequenced.
(BAC clones (80-100 kb long DNA fragments ) arranged in contigs.)
4. CLONE BY CLONE SEQUENCING
19. In this approach, genomic DNA is cut into pieces
Inserted into BAC vectors
Transformed into E. coli where they are replicated
The BAC inserts are isolated
Mapped to determine the order of each cloned fragment.
Each BAC fragment in the Golden Path is fragmented randomly into smaller pieces
Each piece is cloned into a plasmid
Sequenced on both strands.
These sequences are aligned so that identical sequences are overlapping.
5. SHOTGUN SEQUENCING METHOD
This is referred
to as the Tiling
Path.
21. Several draft sequences of the rice genome are also available
and are being extensively used for study of other cereal
genomes
Analyzing & comparing genetic material from different species
Evolution, gene function, and inherited disease
Understand the uniqueness between different species
30. Variety :- Rice (Oriza sativa)
Scientist:- Igno Potrycus &
Peter Boyer.
Produce :- β-varotene
Precursor of Vit. A.
Golden rice was created by transforming rice with two beta-
carotene biosynthesis genes:
psy (phytoene synthase) from daffodil (Narcissus pseudonarcissus)
crtI (carotene desaturase) from the soil bacterium (Erwinia
uredovora)
30
Ye, Xi et al., (2000)
32. Application of candidate gene strategy to
identify CrtRB1 locus
Jiabing et al., (2014), Nature Genetics
33. GENETIC ENHANCEMENT OF NUTRITIONAL QUALITY OF
GRAIN SORGHUM
Genetically enhancing the nutritional quality of grain sorghum by
the introduction of genes encoding the methionine-rich maize beta-
zein and the lysine-rich barley chymotrypsin inhibitor CI-2 proteins.
The goal to produce transgenic sorghum plants with elevated lysine
and methionine contents.
A biolistic and Agrobacterium-mediated transformation protocol
for selected grain sorghum lines was established. This would form
the technological basis for nutritional quality improvement of grain
sorghum.
A Grootboom and M M O’Kennedy (2013)
35. Challenges in using genomics for breeding
Precision phenotyping
Density of genetic maps.
Low heritability of traits.
Contribution of regulatory variation
Consideration of epistasis
Technical skill
Technical difficulties
Cost investment issues
36. Genomics based technologies is producing enormous amounts of
DNA sequence information that is opening up new experimental
opportunities for functional genomics analysis.
The incorporation of metabolomic data and data from phenotype
studies will close the loop and create the foundation for advanced
knowledge.
The recent integration of advances in molecular biology, transgenic
breeding and molecular marker applications with conventional plant
breeding practices has created the foundation for genomic research.
Genomics will affect every aspect of cereal breeding and will
modernize this old science, although genomic approaches will not
succeed unless they are combined with traditional breeding
programs.
37. Some of References
Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q. 2012. Rice functional genomics
research: Progress and implications for crop genetic improvement. Biotechnology
Advances (30) 1059–1070.
Sasaki T, Wu J, Mizuno H, Antonio BA, and Matsumoto T. 2008. The Rice Genome
Sequence as an Indispensable Tool for Crop Improvement. Chapter 1.1,
Springer-Verlag Berlin Heidelberg.
Tyagi AK, Mohanty A. 2000. Rice transformation for crop improvement and functional
genomics. Plant Science (158) 1–18.
Cai Q, Yuan Z, Chen M, Yin C, Luo Z, Zhao X, Liang W, Hu J & Zhang D. 2014.
Jasmonic acid regulates spikelet development in rice. ISSN (online) 2041-
1723.
Varshney R.K., Thiel T., Stein N., Langridge P., Graner A. Cereal Genomics. Cell Mol
Biol Lett 2004; 7: 537-546