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

Maneesha S Saxena,Vinod Kumar,Deepak Bajaj,Mohar Singh,Swarup K Parida,Saurabh Badoni,Kailash C Bansal,Shouvik Das,Alice Kujur,Akhilesh K Tyagi

doi:10.1371/journal.pone.0107484

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.

Highlights

Chickpea [Cicer arietinum (L.)] is one of the most important food legume crops in the world and serves as an important source of protein with essential amino acids in human diet
The functional annotation of experimentally validated informative 334 microsatellite markers- and 380 single nucleotide polymorphism (SNP) markers-containing genes revealed their maximum correspondence with transcription factors (TFs) gene families like bZIP, bHLH and AP2-EREBP (APETALA2 ethylene-responsive element binding proteins) (525, 73.5%), followed by growth and metabolism-related enzymes (170, 23.8%) and expressed proteins (19, 2.7%) (Figure S2)
Natural genetic variation scanned in the wild Cicer, which is expected to be much wider than cultivated species [10], can be transferred from the diverse gene pools of wild accessions to cultivated species to facilitate their genetic improvement through marker-assisted introgression breeding

Summary

Introduction

Chickpea [Cicer arietinum (L.)] is one of the most important food legume crops in the world and serves as an important source of protein with essential amino acids in human diet. The significance of inter-specific hybridization by introducing the desirable target traits of agricultural importance from wild species of primary gene pool to cultivated varieties for enhancing their seed and pod yield and stress tolerance have been demonstrated in chickpea [7,8,10,12]. Producing these successful inter-specific hybrids relied upon combinations of accessions selected from each of the cultivated and wild species for cross-pollination and their level of genetic variability to ascertain suitable cross-compatibility

Methods

Results

Discussion

Conclusion