Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea

Das, S and Upadhyaya, H D and Srivastava, R and Bajaj, D and Gowda, C L L and Sharma, S and Singh, S and Tyagi, A K and Parida, S K (2015) Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA Research. 01-10. ISSN 1340-2838

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Abstract

We developed 21,499 genome-wide insertion–deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60–83%) potential and wider genetic diversity (15–89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-effective agarose gel-based assay. This signifies added advantages of this user-friendly genetic marker system for manifold large-scale genotyping applications in laboratories with limited infrastructure and resources. Utilizing 6,254 InDel markers-based high-density (inter-marker distance: 0.212 cM) inter-specific genetic linkage map (ICC 4958 × ICC 17160) of chickpea as a reference, three major genomic regions harboring six flowering and maturity time robust QTLs (16.4–27.5% phenotypic variation explained, 8.1–11.5 logarithm of odds) were identified. Integration of genetic and physical maps at these target QTL intervals mapped on three chromosomes delineated five InDel markers-containing candidate genes tightly linked to the QTLs governing flowering and maturity time in chickpea. Taken together, our study demonstrated the practical utility of developing and high-throughput genotyping of such beneficial InDel markers at a genome-wide scale to expedite genomics-assisted breeding applications in chickpea.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Flowering time, InDel, Maturity time, QTL
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 22 Sep 2015 09:20
Last Modified: 21 Oct 2016 06:34
URI: http://oar.icrisat.org/id/eprint/9012
Official URL: http://dx.doi.org/10.1093/dnares/dsv020
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors gratefully acknowledge the financial support of the Department of Biotechnology (DBT), Government of India, through their research grant (102/IFD/SAN/2161/2013–14) for this research work. AK and SD acknowledge the CSIR (Council of Scientific and Industrial Research) and DBT for the award of Senior/Junior Research Fellowships. We thank the DNA Sequencing Facility, NIPGR for the automated fragment analysis and sequencing. We are grateful to the editor and reviewers for critically evaluating the manuscript and providing constructive comments for its improvement.
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