Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL -hotspot” region for drought tolerance in chickpea

Jaganathan, D and Thudi, M and Kale, S M and Azam, S and Roorkiwal, M and Gaur, P M and Kavi Kishor, P B and Nguyen, H and Sutton, T and Varshney, R K (2015) Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL -hotspot” region for drought tolerance in chickpea. Molecular Genetics and Genomics, 290 (2). pp. 559-571. ISSN 1617-4623

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To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Drought tolerance; Genotyping-by-sequencing; QTL-hotspot; Fine Mapping; Candidate Genes; CAPS/dCAPS; Marker-assisted breeding
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 03 Jul 2015 10:42
Last Modified: 06 Aug 2018 08:24
Official URL:
Acknowledgement: Technical assistance from Vinay Kumar is greatly appreciated. The work has been undertaken as a part of Australia–India strategic research fund (AISRF) project funded by Department of Science and Technology (DST) and Tropical Legumes I (TLI) project funded by Bill and Melinda Gates Foundation (BMGF) through CGIAR-Generation Challenge Program (GCP; This work has been carried out as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.
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