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Fine mapping of a “QTL-hotspot” for drought tolerance in chickpea (Cicer arietinum L.)

Jaganathan, D., Kale, S., Thudi, M., Ruperao, P., Kavi Kishore, P.B., Gaur, P.M., Mohan Katta, A.V.S.K., Nguyen, H.T., Batley, J., Edwards, D., Sutton, T. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2014) Fine mapping of a “QTL-hotspot” for drought tolerance in chickpea (Cicer arietinum L.). In: 6th International Food Legume Research Conference/7th International Conference on Legume Genetics and Genomics, 7 - 11 July 2014, TCU Place Saskatoon, Saskatchewan, Canada.


To understand the genetic complexity and mechanism of drought tolerance in chickpea, a genomic region (~35 cM) harboring QTL for drought tolerance traits was identified on linkage group 04 (CaLG04) using a linkage mapping based approach. To enhance marker density in this region, two approaches were adopted: (i) genotyping-by-sequencing (GBS) and (ii) re sequencing at low coverage referred to as Skim sequencing. The GBS approach, with 5X and 0.2X coverage on parental lines and 232 RILs, respectively, provided 828 single nucleotide polymorphism (SNP) markers. A total of 49 SNPs were integrated in the “QTL-hotspot” region that narrowed the QTL interval from 35cM to 14 cM (~7 Mb on the physical map). The Skim sequencing approach, with 7-8X and 0.72X coverage on parental lines and 232 RILs respectively, identified 53,175 high quality SNPs utilized to construct a bin map with 1,610 recombination bins. QTL analysis using the bin map and precise phenotyping data split the ~7 Mb QTL into four regions: (i) 13.16-13.23 Mb region harboring 8 candidate genes and QTL for 5 drought tolerance traits; (ii) 13.39-13.54 Mb region harboring 11 candidate genes and QTL for 4 drought tolerance traits (iii) 14.15-14.27 Mb region harboring 11 candidate genes and QTL for pod number (POD) (iv) 14.99-15.08 Mb region harboring 9 candidate genes and QTL for POD. In addition to an approach that will enable further fine mapping of the QTL regions identified, candidate genes ware being characterized for potential to improve drought tolerance in chickpea.

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