Three molecular markering techniques: inter-simple sequence repeat (ISSR); start codon targeted (SCoT), conserved DNA-derived polymorphism (CDDP) markers were compared for fingerprinting of 40 varieties of bread wheat. The number of scoreable and polymorphic bands produced using the ISSR, SCoT and CDDP primers for varieties was more than that of genotypes. Average polymorphism information content (PIC) for ISSR, SCoT and CDDP markers was 0.39, 0.41 and 0.34, respectively, and this revealed that three different marker types were equal for the assessment of diversity amongst genotypes. Cluster analysis for three different molecular types revealed that genotypes taken for the analysis can be divided in three and four distinct clusters. There were no significant differences among these markers in terms of the evaluation of genotypes. These results suggest that efficiency of SCoT, CDDP and ISSR markers was relatively the same in fingerprinting of genotypes but SCoT and CDDP analysis are more effective in fingerprinting of wheat genotypes. To our knowledge, this was the first detailed report of a comparison of performance among two targeted DNA region molecular markers (SCoT and CDDP) in comparision with ISSR technique on a set of samples of wheat cultivars. Overall, our results indicate that SCoT, ISSR and CDDP fingerprinting could be used to detect polymorphism for genotypes of wheat

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.