Helpful presentation for basic genetic improvement technologies in rice improvement in various terms.

1. Applied Genomic Research in RiceApplied Genomic Research in Rice
Genetic ImprovementGenetic Improvement
Lokesh Gour & Lakshman Gupta
Guided by:-Guided by:-
Dr. S.K. Singh, Assistant ProfessorDr. S.K. Singh, Assistant Professor
JNKVV, JabalpurJNKVV, Jabalpur
DEPARTMENT OF PLANT BREEDING & GENETICSDEPARTMENT OF PLANT BREEDING & GENETICS
JAWAHARLAL NEHRU KRISHI VISHWA VIDYALAYAJAWAHARLAL NEHRU KRISHI VISHWA VIDYALAYA
JABALPUR (M.P.)JABALPUR (M.P.)

2. CONTENTS
1.Introduction
2.Genomics
3.Need of Genomic research in rice
4.Conventional to molecular breeding through genomic research
5.5.Laboratories for genomic research in IndiaLaboratories for genomic research in India
6.Tools for Genomic research
7.Technologies for implication of genomics
8.Application areas of genomics research
9.Current status
10.Examples of implication of genomics
11.Conclusion
12. Some of References

3. INTRODUCTION
 Rice is the world’s most important food crop and a staple food for more
than half of the world’s population. More than 90% of the world’s rice is
produced and consumed in Asia, where 60% of the people live.
 In the last six decades, rice production has steadily kept in pace with the
population growth rate, mainly due to the gains from the technologies of
green revolution era such as semi – dwarf, fertilizer responsive high
yielding varieties and other associated managerial technologies.
 Rice is a model crop for genetics and breeding research:-
1. Small genomic size – 45 × 10 bp.⁶
2. Gene bank with 1,00,000 accessions.
3. Highly dense molecular map.
4. Several wild species.
5. Efficient genetic transformation.

4. What is GenomicsWhat is Genomics
??

5. (Genomics word was coined by Thomas Roderick in 1986.)(Genomics word was coined by Thomas Roderick in 1986.)
(Study of structure & function of entire genome of a living organism)(Study of structure & function of entire genome of a living organism)
(Study of the structureStudy of the structure
of entire genome of anof entire genome of an
organism)organism)
(Study of the function(Study of the function
of entire genome of anof entire genome of an
organism)organism)
GENOMICSGENOMICS
Structural GenomicsStructural Genomics Functional GenomicsFunctional Genomics

6. NEED OF GENOMICS IN RICE
Rice demand:
• In each of the next 10 years produce at least 8 million tons rice more
(rough rice) .
Rice supply:
• Little change in harvested area(160 million ha)
• Yield growth of 1.2-1.5% until 2020 (+50-60 kg/ha/yr)
• Yield growth of 1.0-1.2% after 2020
Change how we grow rice:
• New seeds to adapt to changing climate
• Less tillage, less water, less labour, less pesticides, more efficient
fertilizer use
• More resilient, diversified rice-based farming systems
• Is GENOMICS play a role here ?

7.  Rice is the first genome of crop plants sequenced with high precision.Rice is the first genome of crop plants sequenced with high precision.
 The rapid advances in genomic research globally, rice researchThe rapid advances in genomic research globally, rice research
areas summarized in three fronts:areas summarized in three fronts:
 construction of technological and resource platforms for highconstruction of technological and resource platforms for high
throughput gene identification;throughput gene identification;
 functional genomic analysis of agronomic traits and biologicalfunctional genomic analysis of agronomic traits and biological
processes;processes;
 Identification and isolation of functional genes.Identification and isolation of functional genes.
 Rice genome is well mapped & well characterized, estimated 400-Rice genome is well mapped & well characterized, estimated 400-
430 Mb430 Mb

8. ConventionalConventional
breeding to molecularbreeding to molecular
breeding throughbreeding through
genomic researchgenomic research
??

9.  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.
9
From here… …to here
shifted

10. In conventional breeding normally options are present of genes can be
identified when expression where comes during adverse condition

11. By the use of genomic research now we can easilyBy the use of genomic research now we can easily identify theidentify the
presence or absence of gene in early stagepresence or absence of gene in early stage

12.  By the use of molecular markersBy the use of molecular markers exact location of particular geneexact location of particular gene onon
chromosome can easily be identifiedchromosome can easily be identified
 Presence of all of the important genes and related markers will bePresence of all of the important genes and related markers will be
very much helpful to identified and development of newvery much helpful to identified and development of new cultivars ascultivars as
we desire -we desire - Varietal identificationVarietal identification
 Insertion and deletions areInsertion and deletions are desirable or undesirable, easily bedesirable or undesirable, easily be
possible to identifypossible to identify with the sequencing of rice.with the sequencing of rice.

13. Laboratories for genomic research in IndiaLaboratories for genomic research in India
 National Research Centre for Plant Biotechnology, IARI, NewNational Research Centre for Plant Biotechnology, IARI, New
DelhiDelhi
 International Centre for Genetic Engineering & Biotechnology,International Centre for Genetic Engineering & Biotechnology,
New DelhiNew Delhi
 Jawaharlal Nehru University , New DelhiJawaharlal Nehru University , New Delhi
 National Botanical Research Institute , LucknowNational Botanical Research Institute , Lucknow
 Delhi UniversityDelhi University
 ICRISAT and DRR ,HyderabadICRISAT and DRR ,Hyderabad

14. Tools for Genomic ResearchTools for Genomic Research
QTL mapping
DNA sequencing

15. QTL MappingQTL Mapping
Character isolationCharacter isolation
Fine-mappingFine-mapping
Genome scanGenome scan
Using strategies :Using strategies :
o Mapping populationMapping population
o PhenotypesPhenotypes
o GenotypesGenotypes
o Statistical methodologyStatistical methodology

16. Genome sequencing
Sequence analysis
Gel electrophoresis
DNA fragment
elution
Sequencing
reaction (Cycle
sequencing)
Sequence alignment
(using BLAST- Basic
local alignment tool)
Annotation

17. Sr. No. Rice Sequence Participant Chromosome
1. Rice Genome Research Program (RGP), Japan 1 , 6 ,7 , 8
2. Korea Rice Genome Research Program , Korea 1
3. CCW (US)
CUG (Clemson University)
Cold Spring Harbor University
3 , 10
4. TIGR- US 3 , 10
5. PGIR-US 10
6. University of Wisconsin- US 11
7. National Centre of Gene Research
Chinese Academy of Science – China
4
8. Rice Genome Program – University of Delhi 11
9. Academia Sinica Plant Genomic Center (Taiwan) 5
10. Genoscope – France 12
11. Universidad fedral de Pelotas – Brazil 12
12. Kasetsant University – Thailand 9
13. MG Gill University – Canada 9
14. John innescenter – UK 2
Institute which sequenced the particular chromosome at RGPInstitute which sequenced the particular chromosome at RGP

18. Technologies for Implication of Genomics in Rice
Crop Improvement
Marker assisted selectionMarker assisted selection
Gene cloningGene cloning
Genetic EngineeringGenetic Engineering

19. F2
P2
F1
P1 x
TolerantSusceptible
Selection based on presence of marker
Marker Assisted Selection (MAS)
Large population consisting of
thousands of plants

20. Genetic Engineering

21. Gene Cloning
Spikelet morphology of the wild type, eg13, eg11 and F1 progeny from eg13x eg11.
(Scale bars, 1 mm)
Positional cloning of EG1 responsible for Jasmonic acid which regulates
spikelet development in rice

22. Application areas of genomic research in riceApplication areas of genomic research in rice
Yield improvement through quicker & efficient discovery and
dissection of yield enhancing QTLs and their utilization in marker-
assisted breeding/transgenic breeding
Possibility of conversion of rice from a C3 to C4 plant
Understanding the molecular basis of heterosis and cytoplasmic
male sterility
Enhanced availability of agronomically important genes for
transgenic breeding
Unravelling the pathways/networks associated with abiotic stress
tolerance.

23. Fig: 1 - Number of genes
isolated by different methods
Fig: 2 - Functional categories
of the isolated genes
Current status of isolated genes in riceCurrent status of isolated genes in rice

25. Some important genes tagged using molecular
markers
Trait Genes Markers Chromosome
reference
Blast
resistance
Pi-1 RZ 536, RG303, NpB 181 11
Pi-2 RG 64.XNpb 294 6
Bacterial
blight resistant
Xa-1 XNpb 235, XNpb 120 4
Xa-21 Y03700 4
Gall midge Gm(2) RG 329, RG476 4 etc.

26. Gene Trait Country Performance Year
cry1Ab (from
IRRI),
cry1Ac
Insect
resistance
India Good level of
resistance
2002-2005
Xa21 Bacterial
blight
resistance
China & India
(DRR,
Hyderabad).
Excellent field
performance
of
transgenic
IR72 in
response to
BB
2000 &
2002-2004
Bar Herbicide
tolerance
Bayer, India Good level of
tolerance
2005-2007
NHX Salinity
tolerance
India Moderate
level of
tolerance
2005
Gene transformed in IndiaGene transformed in India

27. Characterization of genes controlling Important traitCharacterization of genes controlling Important trait

30. Examples of Implication of GenomicsExamples of Implication of Genomics
in Rice Trait Improvementin Rice Trait Improvement

31. 1. High depth rooting variety development1. High depth rooting variety development
High depth rooting
development using
Dro1 in IR64

32. 2. Salt Tolerant variety development2. Salt Tolerant variety development

33. Fig - Schematic diagram of genetic analysis and fine mapping of low
glutelin content gene in W3660.
3. Low Glutelin content gene in rice3. Low Glutelin content gene in rice

34. 4. QTL for BLB resistance
• Bacterial Leaf Blight caused by Xanthomonas
oryzae pv. Oryzae (Xoo)
• Estimated annual yield loss is 20-60 % (Rice
knowledge portal, 2012)
• BLB is wide spread in irrigated and low land rice
ecosystem. Growing resistant varieties is the only
possible way to tackle the disease.
• More than 30 genes (Xa1, Xa2 …..Xa30)
characterized. Genotypes carrying single resistant
gene have shown susceptibility at different
locations.
• Introgression of multiple R-genes into the genetic
background of elite rice varieties with the help of
closely linked markers can ensure durable
resistance.

35. 5. Bacterial Blight Resistance by MAS5. Bacterial Blight Resistance by MAS
1- Pusa Basmati 1 2- IRBB55
M 1 2 23
950bp
500bp
450bp
xa13 linked marker RG 136
M 1 2 33 M
650bp
950bp
Xa21 linked STS Marker pTA 248
IR24 IRBB13 IRBB21 IRBB55 32-6-7-67 PB-1

36. 6. Biofortified Rice Development

37. 7. QTL for submergence tolerance
• A major QTL (Sub1) for submergence tolerance identified and fine
mapped on chromosome 9 in the submergence tolerant cultivar
FR13A
• Sub1A was strongly induced in the tolerant cultivars in response to
submergence, whereas intolerant cultivars had weak or no induction
of the gene
• The grain quality parameters in the Sub1 lines were on par with the
non- introgressed swarna.

38. •Sub1 variety
testing in farmer’s
field in India &
Bangladesh
•Swarna sub1 is 1st
variety released in
India & Philippines
Farmer’s field inRangpur (Bangladesh)
Sub1 varieties
Susceptible check
Farmer’s tolerant variety
BR11
BR11-SUB1
Swarna
Swarna sub 1
Farmer’s field,Orissa
Gayatri
Gayatri sub 1

39. Function of
sub1 to keep
meristem alive
during stress.
Sub1
Sub1 and
Drought???

40.  The recent integration of advances in molecular biology, transgenicThe recent integration of advances in molecular biology, transgenic
breeding and molecular marker applications with conventional plantbreeding and molecular marker applications with conventional plant
breeding practices has created the foundation for molecular plantbreeding practices has created the foundation for molecular plant
breeding.breeding.
 The trinity of DNA marker technology, genetic engineering willThe trinity of DNA marker technology, genetic engineering will
certainly accelerate rice improvement programmes across the worldcertainly accelerate rice improvement programmes across the world
including India.including India.
 Through a judicious application of all these technologies, developmentThrough a judicious application of all these technologies, development
of a designer rice plant which is high yielding, using lesser nutrientsof a designer rice plant which is high yielding, using lesser nutrients
from soil, with tolerance to biotic and abiotic stress and with enhancedfrom soil, with tolerance to biotic and abiotic stress and with enhanced
nutritional quality may be possible in the near future.nutritional quality may be possible in the near future.
 There is an urgent need to integrate the recent technology work withThere is an urgent need to integrate the recent technology work with
mainstream plant breeding to derive maximum benefits from themainstream plant breeding to derive maximum benefits from the
wonderful science of genomic research.wonderful science of genomic research.
CONCLUSION

41. 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.

42. Thank You