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 assay 615 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