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Fine mapping studies identified a 113 kb region within “QTL-hotspot_a” for seed weight and drought related traits in chickpea

Kale, S.M., Jaganathan, D., Roorkiwal, M., Thudi, M., Purushothaman, R., Praveenkumar, M., Krishnamurthy, L., Kavi Kishor, P.B., Gaur, P.M. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2017) Fine mapping studies identified a 113 kb region within “QTL-hotspot_a” for seed weight and drought related traits in chickpea. In: InterDrought-V, 21 - 25 February 2017, Hyderabad, India.


A “QTL-hotspot” region of 7 Mb size for drought component traits was identified on CaLG04, using a recombinant inbred line (RIL) population (ICC 4958 × ICC 1882) in chickpea. Further, skimbased genotyping by sequencing (GBS) approach with large SNP markers delimited the “QTL-hotspot” region into two sub-regions; viz, “QTL-hotspot_a” of 139.22 kb and “QTL-hotspot_b” of 153.36 kb, on the kabuli draft genome sequence. In order to validate and identify more recombinations in the sub-regions for further refinement, a fine mapping population with 1,911 lines was developed. Flanking markers of the two “QTL-hotspot” sub-regions were converted to KASPar assays and used to screen the fine mapping population consisting of 1,911 lines. As a result, 19 F2:3 recombinant families were identified. These families were phenotyped for seed weight and other drought-related traits. Comparison of genotype and phenotype data identified a genomic region of ~113 Kb size within “QTL-hotspot_a” responsible for 100 seed weight (100SDW) and other drought-related traits in chickpea. Subsequently, a syntenic study between the refined “QTL-hotpsot” region and desi genome identified a 2 Mb region on Ca_LG_4 pseudomolecule. Whole genome re-sequencing (WGRS) analysis of selected lines from each recombinant family identified several non-synonymous and InDel mutations within important candidate genes. Functional validation of these genes will help decipher the mechanism of drought stress tolerance in chickpea.

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