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

Publication Overview
TitleGenome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea
AuthorsDas S, Upadhyaya HD, Srivastava R, Bajaj D, Gowda CL, Sharma S, Singh S, Tyagi AK, Parida SK
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Volume22
Issue5
Year2015
Page(s)377-386
CitationDas S, Upadhyaya HD, Srivastava R, Bajaj D, Gowda CL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea. DNA research : an international journal for rapid publication of reports on genes and genomes. 2015 Sep 17; 22(5):377-386.

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.

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Projects
This publication contains information about 1 projects:
Project NameDescription
chickpea-Indel_Genome-Das-2015
Featuremaps
This publication contains information about 2 maps:
Map Name
chickpea-ICC4958xICC17160
chickpea-ICC4958
Properties
Additional details for this publication include:
Property NameValue
ISSN1756-1663
Journal AbbreviationDNA Res.
LanguageEnglish
Language AbbrENG
Publication Date2015 Sep 17
Publication ModelPrint-Electronic
Publication TypeJournal Article
Copyright© The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
eISSN1756-1663
Elocationdsv020