A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

Bajaj, D and Upadhyaya, H D and Khan, Y and Das, S and Badoni, S and Shree, T and Kumar, V and Tripathi, S and Gowda, C L L and Singh, S and Sharma, S and Tyagi, A K and Chattopdhyay, D and Parida, S K (2015) A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Scientific Reports, 5 (9264). pp. 1-14. ISSN 2045-2322

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Abstract

High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Genome Mapping; Chickpea; QTL mapping; Genotyping
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 22 Jul 2015 06:18
Last Modified: 21 Oct 2016 06:21
URI: http://oar.icrisat.org/id/eprint/8892
Official URL: http://dx.doi.org/10.1038/srep09264
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors gratefully acknowledge the financial support by the Department of Biotechnology (DBT), Government of India, through their research grant (102/IFD/SAN/2161/2013-14) for this research work. SD acknowledge the DBT for Junior Research Fellowship award. We thank the DNA Sequencing Facility, NIPGR for automated fragment analysis and sequencing.
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