Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea

• Published in: PloS one 2014-09, Vol.9 (9), p.e107484-e107484
• Main Authors: Saxena, Maneesha S, Bajaj, Deepak, Kujur, Alice, Das, Shouvik, Badoni, Saurabh, Kumar, Vinod, Singh, Mohar, Bansal, Kailash C, Tyagi, Akhilesh K, Parida, Swarup K
• Format: Article
• Language: English
• Subjects: Agricultural production; Alleles; Barley; Biology and Life Sciences; Brassica napus; Breeding; Chromosome Mapping; Cicer; Cicer - genetics; Cicer arietinum; Cultivars; Deoxyribonucleic acid; DNA; Domestication; Fluorescence; Fluorescent indicators; Gene polymorphism; Gene pool; Genetic aspects; Genetic diversity; Genetic improvement; Genetic markers; Genetic structure; Genetic Variation; Genetics; Genomes; Genomics; Genotype; Genotyping; Germplasm; Glycine max; Haplotypes; Hybridization; Ionization; Legumes; Linkage disequilibrium; Linkage Disequilibrium - genetics; Markers; Microsatellites; Morphology; Phenotype; Phylogenetics; Polymorphism; Polymorphism, Single Nucleotide - genetics; Recombination; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0107484

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.