title: Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea.
abstract: Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Maneesha S
authors.initials: MS
authors.lastname: Saxena
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Alice
authors.initials: A
authors.lastname: Kujur
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Badoni
authors.affiliation: National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India.
authors.forename: Mohar
authors.initials: M
authors.lastname: Singh
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India.
authors.forename: Kailash C
authors.initials: KC
authors.lastname: Bansal
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 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, India.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics*; D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D015810:Linkage Disequilibrium / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics