What is happening
in peanut genomics
in India
Rajeev Varshney
Senior Scientist- Applied Genomics, ICRISAT
Coordinator, Indian Groundnut Genomics Consortium
Leader, Comparative Genomics & Gene Discovery
(Generation Challenge Programme)
Groundnut production in India
• 1st most important oilseed crop in India
Area: 6.6 million ha
Production: 5.9 million t
Productivity of groundnut – 0.97 t ha-1
~ 20% of world production comes from India alone!
Constraints in production
Drought
Leaf
spot
Rust
Indian Groundnut
Genomics Consortium
- Indian Council of Agricultural Research
Three main partners:
ICRISAT, Patancheru, A.P.
(Intern. Crops Res. Inst. Semi-Arid Tropics)
NRCG, Junagadh, Gujarat
(National Research Centre for Groundnut)
UAS, Dharwad, Karnataka
(University of Agricultural Sciences)
Team of multidisciplinary scientists
Activities
• Generation of microsatellite-enriched libraries and
identification of ~500 microsatellite or simple sequence
repeat (SSR) loci
• Generation of groundnut unigene-derived SNP markers and
development of cost effective CAPS assay
• Construction of integrated genetic maps with SSR, SNP
and DArT markers
• Phenotyping of mapping populations at three locations
(ICRISAT, NRCG, UASD) over 3 years
• Identification of genes/QTLs associated with resistance
to foliar diseases (rust and late leaf spot) and tolerance to
drought (TE, SCMR and SLA)
What we already have done at ICRISAT…
SSR marker development
 In silico approach after mining sequence data
- Aeschynomenoid/ Dalbergoid and Genistoid clades of
the Leguminoae (15 genera)
- 6 genera Adesmia, Amorpha, Dalbergia, Chaetocalyx
Lupinus and Stylosanthes: 411 seqs contained SSRs
.
- Primer pairs for 109 unique SSRs
- 79 functional in one of six genera
- 51 primer pairs functional in peanut
 BAC-end sequence derived SSRs (Doug Cook)
Genetic map construction
Ah1
Ah2
0.0
GM635a
5.9
GM635b
seq18G09_5B
seq13A07
GM669
seq17E01
10.7
11.6
14.5
19.0
0.0
3.3
6.2
7.6
9.4
14.5
Ah3
GM630
seq10D04
RN6F05
GM633
PM179
TC6E01
GM626
0.0
seq16C06
15.5
seq13E09
30.3
42.6
Ah10
seq2B09
GM672
TC2D06
GM667
Ah5
TC3G01b
0.0
XIP219
XIP606
XIP419
XIP123
PM721
GM660
GM679
XIP177
XIP406
TC9F10_8A
TC6H03_6B
PM733a
18.0
24.3
26.5
28.1
29.2
29.8
31.5
33.8
35.9
37.4
39.2
40.9
TC3G01a
TC3G01c
48.4
50.1
Ah9.2
Ah4
0.0
13.9
Ah11
XIP287
0.0
Ah12
TC11B04
23.6
27.1
seq19D06
37.3
GM723b
43.7
seq19H03
GM647
0.0
TC7C06
11.0
XIP245
16.4
18.9
22.6
GM623
TC1A02_7B
XIP689
28.4
TC1A01
34.8
PM377
38.6
seq9H08a
46.1
XIP171A
Ah15
Ah14
TC4D09
0.0
PM427
0.0
XIP105
PM375
GM629
GM736
XIP108A
XIP524
7.7
10.8
13.2
6.7
10.3
22.5
24.6
seq19A05
XIP165
23.9
26.1
seq18C05
XIP108B
Ah8
Ah7
0.0
RI1F06_2A
8.6
seq18E07
17.1
18.9
seq1B09
PM499
25.3
PM73
34.6
AC2C05
0.0
seq18G01
9.8
seq19D01
0.0
22.5
50.8
seq2G04
62.0
TC9F04
Ah16
0.0
seq9G05
Ah193_1A
Ah6
0.0
Ah17
TC4G02
Ah9.1
GM698
seq8H01
Ah18
0.0
GM624
5.4
9.0
seq19B12
TC9H09
20.1
seq15C10
0.0
3.8
0.0
seq7G02
18.6
20.7
22.7
26.8
28.8
gi1170_9A
Lec1_9A
PM436
GM694
seq14H06
34.5
TC5A06
Ah19
seq11G03
TC4F12_2A
0.0
Ah9.2
Ah10
0.0
seq2B09
0.0
XIP
14.6
16.2
GM672
TC2D06
13.9
seq
23.6
Ah193_1A
27.1
seq
37.3
GM
43.7
seq
61.8
PM
75.6
PM
32.9
seq13A10
Ah20
seq19D09_1B
0.0
GM641
seq13A10
42.1
36.7
GM618
51.9
Gi4926
62.9
GM745
67.5
seq18A05
83.0
seq19G07
35.4
TC7E04
TC7H11_2A
Collab.
D Bertioli, Brazil
G He, USA
S Knapp, USA
47.3
61.8
75.6
PM183
60.8
GM692
61.1
XIP136
PM418
Cultivated x Cultivated
TAG 24 x ICGV 86031 -RIL
seq16G08
Mapping water use
efficiency QTLs
Molecular diversity
916 accessions at 21 SSR loci
fastigiata: 488
hypogaea: 321
wild: 47
Reference collection
(300 genotypes)
Exploring association
genetics approach
What we plan to do at ICRISAT
(under Troplical Legume Genomics project)…
Generation Challenge Programme
(www.generationcp.org)
• Launched in August 2003
• 10-year framework (2004–2008; 2009–2013)
• About US$16M annual budget
– 75% Research
– 15% Training and capacity building
– 10% Management cost
• Major donors
– European Community
– DFID
– The Bill & Melinda Gates Foundation
– World Bank
– Switzerland
• Target areas: Marginal drought-prone environments
– Africa (SSA)
– South and South East Asia
– Latin America
• Mandate crops (CGIAR) – 22 crops
• A CGIAR Challenge Programme hosted at CIMMYT, Mexico
GCP Research Structure
Director:
Jean-Marcel Ribaut
SP4
DB, Information Network
(SPL: T van Hintum)
Phenotyping
Phenotyping
SP1
Germplasm
SP2
Gene Discovery
SP3
MAS
(SPL: J-C Glaszmann)
(SPL: R K Varshney)
(SPL: P Monneveux)
SP5
Training/Capacity
(SPL: C de Vicente)
Breeding programmes
(Delivery plans)
Improved genotypes
Improved germplasm in farmers’ fields
Tropical Legume I project
(GCP)
US $ 11 m
Objectives 1-4
Activity 1:
Explore
Diversity
Objective 5
+ Activity 2:
Generate
Genomic
Resources
Activity 3:
Activity 4:
Activity 5:
Identify Marker Identify Marker Improve
Development
Development Germplasm
(Biotic)
(Abiotic)
Development
Objective 6
Peanut
Cowpea
Common bean
Chickpea
Comparative Genomics
Training
Objective 1- Peanut
(PI: Dave Hoisington)
Project Activities
• Develop germplasm for genetic studies and modern
breeding
– Bonny Ntare (ICRISAT, Mali)
• Generate genomic resources for genetic studies and
modern breeding
– Andy Paterson (University of Georgia, USA)
• Identify molecular markers and genes for biotic stress
resistance
– David Bertioli (Catholic University, Brazil)
• Identify molecular markers and genes for drought
tolerance
– Vincent Vadez (ICRISAT, India)
• Improve locally adapted germplasm for target traits
through modern breeding
– Emmanuel Monyo (ICRISAT, Malawi)
Objective 5- Cross species
(PI: Doug Cook)
Objective 5:
Develop cross species resources for comparative genomics in tropical crop legumes
Activity 1:
Comparative Marker Development
Milestones:
Activity 2:
Milestones:
Activity 3:
Milestones:
Doug Cook
1. Development of molecular marker database and web interface.
2. Development of 500 orthologous gene markers.
3. Associate genetic markers to bacterial artificial chromosome clones in each species
Analysis of the Arachis-species Complex
David Bertioli
4. Diploid Arachis AA bacterial artificial chromosome clone end sequencing and SSR discovery
5. Mapping of orthologous genetic markers in diploid Arachis AA population
6. Identification of ultra-long SSRs in tetraploid Arachis
7. Genetic mapping of ultra-long SSRs in tetraploid Arachis
Estimating Genome Divergence at Orthologous Loci
Andy Paterson
8. DNA sequencing and divergence estimates for network of orthologous bacterial artificial chromosome clones
Project partners
• Catholic University of Brasilia, Brazil
• Chitedze Research Station, Department of
Research and Development, Ministry of
Agriculture, Malawi
• EMBRAPA, Brazil
• ICRISAT, India/Malawi/Mali
• Insitut National de Recherche Agronomique du
Niger (INRAN), Niger
• Institut Sénégalais de Recherche Agricole (ISRA),
Senegal
• Naliendele Research Station, Department of
Research and Development, Ministry of
Agriculture, Tanzania
• University of Georgia, USA
Take home message




Community efforts
Rapid advances in genomics
Genome infrastructure available
Applications to breeding
Contributions and thanks
Genomics:
Rajeev Varshney
Dave Hoisington
Gautami, Ravi, Bryan, SomaRaju
Genetic resources:
Hari Upadhyaya
Ranjana Bhattacherjee
Breeding:
Shyam Nigam, R Aruna
Crop Physiology:
Vincent Vadez
Statistics & Bioinformatics:
Subhash Chandra, Jayashree
Collaboartions in India:
NRC for Groundnut: T Radhakrishnan
UAS Dharwad: MVC Gowda, Khedikar
OVERSEAS COLLABORATIONS
UC-Davis: Doug Cook, R Varma
Catholic Univ: David Bertioli
Tuskegee Univ: Guaho He
Univ of Georgia: Steve Knapp
Financial support:
National Fund,
Indian Council of
Agricultural Research
Generation
Challenge
Programme
Department of
Biotechnology