Large scale genomic resources including draft genome sequence, re-sequencing of 90 lines, comprehensive transcriptome assembly and high density genetic maps have been developed for chickpea. Linkage mapping and genome wide association studies (GWAS) are being used for trait mapping. 26 Feb 2014

1. Inclusive Market-Oriented Development (IMOD) –
our approach to bringing prosperity in the drylands.
ICRISAT is a member of the CGIAR Consortium.
Large scale genomic resources including draft genome sequence, re-sequencing of 90 lines, comprehensive transcriptome assembly and high
density genetic maps have been developed for chickpea. Linkage mapping and genome wide association studies (GWAS) are being used for trait
mapping. One genomic region (“QTL-hotspot”) harboring QTLs for several drought tolerance traits has been identified and genotyping-by-sequencing (GBS)
approach is being used to fine-map this region. Introgression of this region in to elite chickpea lines have shown yield improvement under irrigated as well as
rainfed conditions. Similarly QTLs controlling important biotic stresses like Fusarium wilt (FW) and Ascochyta blight (AB) have been mapped and used for
introgression. In parallel, association mapping approaches using genotyping data for 1882 markers and sequence data for 10 genes together with phenotyping data
for 24 drought tolerance traits on the reference set comprising 300 genotypes provided 335 significant marker-trait associations (MTAs). In addition, 5X- 10X
coverage whole genome re-sequencing data have been generated on the reference set that is being used for GWAS analysis. In order to deploy genomic selection, a
training population of 320 elite breeding lines was phenotyped at two locations for yield related traits. Generated genome-wide marker profiling data (Total >3000
markers) along with phenotyping data was used with a range of regression and bayesian based statistical methods to predict genomic estimated breeding values.
Furthermore, several transcriptomics and functional genomics approaches such as RNA-seq, Massive Analysis of cDNA Ends (MACE) with parental genotypes of
mapping populations as well NILs have provided some candidate genes for biotic and abiotic stress response that are being validated through quantitative real time
PCR (qRT-PCR) and TILLING approaches. Genetic mapping of these candidate genes may provide perfect markers for use in chickpea molecular breeding.
Abstract
Molecular markers and genotyping platforms
547 –GSSs
from enriched library
25,000 BAC-end
sequences
2,460 markers
435,018
FLX/454 STRs
SSRs
identified 3,728 26,252 6,845 643
Primer-pairs
synthesized
77 728 1,344 311
20,162
ESTs
Novel SSR markers
SSRs
768 SNPs GoldenGate assay615 SNPs based on legume COSs
153 SNPs from allele specific sequencing 2,068 KASPar assays
>10,000 SNPs based on Solexa sequencing 742 CAPS markers
SNPs 96 VeraCode assays
DArT arrays DArT arrays with 15,360 features/DArT seq
Genome sequencing, re-sequencing and GWAS
Reference genetic map
Mapping population ICC 4958 × PI 489777
Marker loci mapped 1,291
Total map distance (cM) 845.56
Trait mapping
C 214 × ILC 3279 - Ascochyta blight (AB)
C214 × WR 315: Fusarium wilt (FW)
LG 1 LG 2 LG 3 LG 4 LG 5 LG 6 LG 7 LG 8
Drought tolerance Disease resistance
ICC 4958 × ICC 1882 Consensus map ICC 283 × ICC8261
Functional validation of candidate genes
TILLING population development
and allele mining
Morphological mutants in field (M3 generation)
NCBI
41,984
ESTs
ICC 4958
(NIPGR)
97,257
Sanger reads
134.99 Million
Illumina tags
7,127,750 FLX/454 STRs
ICC 4958
(NIPGR)
ICC 4958
(ICRISAT)
103,215 TUSs 34,760 TUSs
46,369 TACs
Amit, Cr5-10
CDC Frontier, CDC Xana,
ICC 12512-1, ICCV 96029,
ILWC 118, Y9563-28
(NRC)
AAFC
CDC Frontier
(NRC)
Comprehensive transcriptome assembly
Allelic variants in Ca220909 gene
Genomic selection
Varshney RK1*, Kudapa H1, Roorkiwal M1, Thudi M1, Chitikineni A1, Odeny DA2, Sabbavarapu MM1, Jaganathan D1, Singh M1,
Katta KM1, Agarwal G1, Khan AW1, Ganga Rao NVPR2, Gaur PM1, Upadhyaya HD1, Rathore A1, Krishnamurthy L1, Shah TM1,
Sharma M1, Samineni S1, Siambi M2, Waliyar F3
Next generation genomics for chickpea
(Cicer arietinum L.) improvement
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2ICRISAT, Nairobi, Kenya;
3ICRISAT, Bamako, Mali; *Address for correspondence: r.k.varshney@cgiar.org
PPI predicted for MYB1R1
qRT-PCR validation
Global distribution of reference set
<7X, 8 7X-8X, 10
8X-9X, 40
9X-10X, 106
10X-11X, 81
11X-12X, 25
>12X, 30
Re-sequencing of reference set
 Illumina sequencing used to generate
153.01 Gb
 73.8% of the genome captured in
scaffolds
 Genome analysis predicted 28,269
genes
 > 81,845 SSRs and 1.97 million variants
 Assembly contains 187 disease
resistance gene homologs
 90 cultivated and wild genotypes re-
sequenced
Draft genome sequence
Genome wide association scan for 100 seed weight
Training
Population
Two locations
IARI
ICRISAT
Two seasons
2011-12
2012-13
Two treatments
Irrigated
Rainfed
KASPar (651)
DArT arrays (15,360)
DArT-Seq
Training Population: 320 elite breeding lines
KASPar: 67 polymorphic out of total 651
DArT: 1432 polymorphic out of 15,360
DArTseq:1684 polymorphic
Control