Abstract
To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past.
Highlights
Many crops that are grown across multiple regions have limited genetic diversity due to bottlenecks from domestication, selective breeding and in some taxa, natural processes [1,2,3,4]
Single nucleotide polymorphism (SNP) markers were highly polymorphic across this diverse set and a total of 611 SNPs were found polymorphic
SNPs were developed using cultivated chickpea and later used for genotyping the wild species, which may account for the greater number of missing loci in the tertiary gene pool and the bimodal distribution of polymorphism information content (PIC) values
Summary
Many crops that are grown across multiple regions have limited genetic diversity due to bottlenecks from domestication, selective breeding and in some taxa, natural processes [1,2,3,4]. Recurrent selection of improved cultivars over multiple generations results in an increasingly narrow genetic base for a crop, making it more vulnerable to disease and limiting its adaptability. Such genetically depauperate crops could have disastrous consequences in the face of emerging diseases and climate change [5,6]. Recent applications of genome mapping suggest that the genetic diversity stored in germplasm banks can be utilized with a much higher level of efficiency than previously imagined [6,7] This is true for self-pollinated crops like chickpea (Cicer arietinum). Such estimates are critical for providing insight into efforts to introgress wild germplasm into elite lines, and for guiding future collections of wild germplasm [10]
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