Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Kujur, A and Upadhyaya, H D and Shree, T and Bajaj, D and Das, S and Saxena, M S and Badoni, S and Kumar, V and Tripathi, S and Gowda, C L L and Sharma, S and Singh, S and Tyagi, A K and Parida, S K (2014) Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea. Scientific Reports, 5 (9468). pp. 1-13. ISSN 2045-2322

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Abstract

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Genetic linkage maps; High-quality SNPs;RIL mapping
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 22 Jul 2015 05:58
Last Modified: 21 Oct 2016 05:38
URI: http://oar.icrisat.org/id/eprint/8891
Official URL: http://dx.doi.org/10.1038/srep09468
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors gratefully acknowledge the financial support for this research study provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14). Alice Kujur and Shouvik Das acknowledge the CSIR (Council of Scientific and Industrial Research) and DBT for Junior/Senior Research Fellowship awards. Authors declare no conflict of interest. Supplementary information accompanies this paper at http://www.nature.com/ scientificreports
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