Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Development Of Genomics Tools For Enhancing Drought Tolerance In Chickpea (Cicer arietinum L.).

Pavana J Hiremath^1,2 , Spurthi N Nayak^1,2 , Andrew D Farmer³ , Srivani Gudipati¹ , Jimmy E Woodward³ , Lekha Pazhamala¹ , Nicy Varghese¹ , Mahender Thudi¹ , Amit Deokar⁴ , Balaji Jayashree¹ , Junichi Kashiwagi¹ , Pooran Gaur¹ , Yongli Xiao⁵ , Polavarapu Kavi Kishor² , Pradeep K Jain⁴ , Ramamurthy Srinivasan⁴ , Peter Winter⁶ , Dave A Hoisington¹ , Chris D Town⁵ , Doug R Cook⁷ , Greg D May³ , Rajeev K Varshney¹

¹  International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru-502324, India

²  Osmania University, Hyderabad- 500 007, India

³  National Centre for Genome Resources (NCGR), Santa Fe, NM 87505 USA

⁴  National Research Centre on Plant Biotechnology (NRCPB), New Delhi-110012, India

⁵  The J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA

⁶  GenXPro GmbH, D60438 Frankfurt, Germany

⁷  University of California, Davis, CA 95616-8680, USA

In order to enhance drought tolerance in chickpea, a variety of genomic tools are being generated for identification of genes/QTLs for prolific and deep root system. A total of 1,655 novel SSRs have been isolated from the SSR-enriched library (311) and BAC-end sequences (1,344) and are being used to map root trait QTLs in ICC 4958 × ICC 1882 mapping population. For identification of drought responsive genes, >10,000 Sanger ESTs have been generated from these parental genotypes. In parallel, the cDNA pools for these parental genotypes assembled from root tissues after imposing drought stress have been sequenced using Solexa technology. Half run of Solexa on cDNA pools of ICC 4958 and ICC 1882 provided 5.2 × 10⁶ and 3.6 × 10⁶ sequence reads of 36 bp length, respectively. Alignment of these Solexa tags with Medicago- IMGAG gene assembly and available transcriptome sequence data for chickpea and other related legume species has provided high confidence SNPs in >500 genes. The primer pairs for these genes designed based on Medicago genome are currently being used to validate SNPs using Sanger sequencing methodology. To improve alignment of Solexa datasets and SNP identification efficiency, >450,000 FLX/454 reads have been generated from a normalized cDNA pool of >20 tissues that have provided >30,000 contigs. Genetic mapping of newly developed and existing SSR markers in public domain together with identified gene-based SNPs should provide candidate markers/genes associated with QTLs for drought tolerance to use them in molecular breeding for chickpea improvement.