Establishing genomics-assisted breeding foundation in chickpea for enhancing crop productivity in Africa and Asia

A Chickpea, an important food legume is generally grown in marginal environments of semi-arid regions of Asia and Africa where the crop production is heavily challenged by abiotic stresses such as terminal drought and biotic factors like legume pod borer (Helicoverpa armigera), fusarium wilt and ascochyta blight. With an objective to tackle these production constraints through molecular breeding, in collaboration with several partners around the world, significant genomic resources have been developed recently (http://www. icrisat. org/gt-bt/ICGGC/homepage. htm). For instance, 1,655 novel SSRs have been isolated from the SSR-enriched library (311) and BAC-end sequences (1,344), a DArT array has been developed with> 16,000 features and> 20,000 ESTs from drought and salinity stress challenged tissues based on Sanger sequencing. Further, a set of 443,969 sequence tags were generated through FLX-454 sequencing from a pool of normalized cDNA assembled from developmental stages and abiotic stresses challenged tissues of a reference chickpea genotype (ICC 4958). Analysis of Sanger as well as FLX-454 sequence data provided 103,215 tentative unique sequences (TUSs). In parallel, transcriptomes of drought and Helicoverpa challenged tissues were sequenced using Solexa sequencing approach. Over 37 million drought responsive tags were obtained from ICC 4958 and ICC 1882 and their alignment with the TUSs provided 26,083 nucleotide variants (SNPs) between the two genotypes. Similarly, 81.2 million tags were generated from Helicoverpa challenged tissues of ICCC 37 and ICC 506 genotypes and a total of 65,536 nucleotide variants were identified..