title: Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.
abstract: We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.
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: 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: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Badoni
authors.affiliation: National Research Centre on Plant Biotechnology (NRCPB), New Delhi-110012, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi-110012, India.
authors.forename: Mohar
authors.initials: M
authors.lastname: Singh
authors.affiliation: National Bureau of Plant Genetic Resources (NBPGR), New Delhi-110012, 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 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.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D029863:Cicer / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA