title: Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea.
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.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Rishi
authors.initials: R
authors.lastname: Srivastava
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: C L L
authors.initials: CL
authors.lastname: Gowda
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Sube
authors.initials: S
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India swarup@nipgr.ac.in swarupdbt@gmail.com.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics*; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics; D060005:Genotyping Techniques; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: InDel; QTL; chickpea; flowering time; maturity time