Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

• Published in: Scientific reports 2015-07, Vol.5 (1), p.12468-12468, Article 12468
• Main Authors: Bajaj, Deepak, Das, Shouvik, Badoni, Saurabh, Kumar, Vinod, Singh, Mohar, Bansal, Kailash C., Tyagi, Akhilesh K., Parida, Swarup K.
• Format: Article
• Language: English
• Subjects: 45/22; 45/23; 45/29; 631/449/1870; 631/449/2492; Alleles; Chromosome Mapping; Chromosomes, Plant; Cicer - classification; Cicer - genetics; Cloning; Domestication; Gene mapping; Gene pool; Genetic diversity; Genetic Variation; Genome, Plant; Genomes; Genotype; Genotyping; Humanities and Social Sciences; Linkage Disequilibrium; Microsatellite Repeats; Molecular Sequence Annotation; multidisciplinary; Phenotype; Phylogeny; Polymorphism, Single Nucleotide; Population genetics; Quantitative Trait Loci; Science; Sequence Analysis, DNA; Single-nucleotide polymorphism; Transcription factors
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep12468

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.