Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea  (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

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.

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

“…The mean heterozygosity, calculated across a number of loci, is a true indicator of the degree of genetic variation within a population [30], implying there is low genetic variation in cowpea. This is expected since cowpea is primarily a self-pollinated crop exhibiting high degree of inbreeding [6,23,31], which reduces genetic diversity.…”

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

“…The mean heterozygosity, calculated across a number of loci, is a true indicator of the degree of genetic variation within a population [30], implying there is low genetic variation within the cowpea accessions. This is expected since cowpea is primarily a self-pollinated crop and exhibits high degree of inbreeding [6,23,31], which reduces genetic diversity.…”

Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea

“…In the smaller subset of 91 genotypes, we also identified three subpopulations (Supplementary Figures 1A-D). Four subpopulations were recently reported in a diverse set of 186 genotypes (including 20 Iranian landraces and 166 Kabuli advanced breeding lines from ICRISAT and ICARDA) using DArTseq markers (Farahani et al, 2019). Two subpopulations were reported in a set of 92 (77 landraces and five elite cultivars) chickpea germplasm lines that represent arid, semi-arid, and FIGURE 3 | GWAS signal for manganese concentration in mature leaves.…”