Abstract
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
Highlights
Chickpea (Cicer arietinum L.) is an important legume food crop that is currently cultivated in wide ranges of climatic regions across the world in more than 45 countries [1]
Classical breeding techniques based on morphological traits able to characterize genotypes based on their phenotypic characters, but these markers are limited in number, influenced by environment, and often have epistatic interaction with other traits
The 186 chickpea genotypes were analyzed by DArTseq-single nucleotide polymorphism (SNP)
Summary
Chickpea (Cicer arietinum L.) is an important legume food crop that is currently cultivated in wide ranges of climatic regions across the world in more than 45 countries [1]. Chickpea is a self-pollinated diploid (2n = 2x = 16) plant with an approximate genome size of 931 Mbp [3] and comprises two types, Desi and Kabuli cultivars, that are distinctly different in agro-morphological characteristics such as seed shape, flower color, growth habit, and genome composition [2,4,5]. Both types of chickpea genotypes are grown worldwide, but Desi type is mainly cultivated in Ethiopia and Indian subcontinent [3]. Different DNA markers such as random amplified polymorphism DNA (RAPD) [9,10,11], inter-simple sequence repeat (ISSR) [12,13], amplified fragment length polymorphism (AFLP) [14,15], and simple sequence repeats (SSR) [16,17]
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