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Developing genomic resources for enabling genomics-assisted breeding in Chickpea (Cicer arietinum L.)

Varshney, R.ORCID: 0000-0002-4562-9131, Nayak, S., Hiremath, P., Thudi, M., Sivakumar, C., Woodward, J., Thakur, V., Gujaria, N., Jahnavi, K., Srivani, G., Farmer, A. and Kashiwagi, J. (2010) Developing genomic resources for enabling genomics-assisted breeding in Chickpea (Cicer arietinum L.). In: Plant & Animal Genome Conference XVIII, 9 - 13 Jan. 2010, San Diego, CA.


A With an objective of realizing genomics-assisted breeding in chickpea, a significant amount of genomic resources is being developed as community efforts ( These resources include: (i) 1,655 novel SSRs from the SSR-enriched library and BAC-end sequences, (ii) DArT array with >16,000 features, (iii) 768 COS-based SNPs and (iv) >20,000 Sanger ESTs and 435,018 FLX-454 reads that provides 103,215 tentative unique sequences (TUSs). Furthermore, over 100 million Solexa tags have been generated from drought and Helicoverpa challenged tissues of four genotypes. Alignment of these Solexa tags with the TUSs provided >50,000 SNPs that will be used to develop a generic SNP genotyping platform. By using a variety of markers and genotyping data from collaborators, an integrated reference genetic map comprising >1800 marker loci has been developed for an interspecific mapping population (C. arietinum ICC 4958 × C. reticulatum PI 489777). In order to identify drought tolerance QTLs, phenotypic data for root traits for two environment and genotypic data for 294 SSR markers were obtained on an intraspecific mapping population (ICC 4958 × ICC 1882). Marker-trait analysis on these has revealed several QTLs for drought related traits and one major QTL contributing ~30% phenotypic variation for root traits is being introgressed into three elite chickpea lines (JG 11, ICC 92318 and KAK 2) using marker-assisted backcrossing (MABC), to develop superior cultivars with enhanced drought tolerance. In summary, genomic resources developed at such a large scale have already started to impact chickpea breeding and will greatly facilitate chickpea improvement in coming years.

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