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.
Flax (Linum usitassimum L.) of family Linaceae is one of the most important crops, which has been widely used from ancient times. The aim of the study was to examine seed morphological characteristics and fatty acids differences among 13 populations of flax (11 from Iran, one from Turkey and one from USA). We studied six morphological variables of seeds in 50 replications. The methyl esters of seeds fatty acids were analyzed using GC. We detected that the flax seeds shape and color were stable among the populations, whereas ANOVA proved significant variations for all the quantitative seed morphological features. Moreover, we found the main fatty acids of the seed oil remained consistent over the ecological and geographical ranges of the populations, except for Khorasan and Turkey populations differed from the rest by their second main fatty acid. We registered that the amounts of main fatty acids differed among the populations and ANOVA test proved significant differences for most of the identified fatty acids. In addition, significant relationships were registered between some fatty acids. The populations were clustered in UPGMA tree and PCO plot into three distinct groups. CA joined plot and PCA biplot demonstrated that each group had specific type and amount of fatty acid. Therefore, we defined three chemotypes: petroselinic acid, linoleic and linolenic acids, and oleic acid. Although, studied ecological factors influenced some fatty acids amounts, populations from different phytogeographical regions clustered closely as chemotypes. This revealed that populations of each chemotype have been originated from the same diversity center, and some secondary diversity centers exist for flax in the world.
Ascochyta blight (caused by Ascochyta rabiei) is an important disease of chickpea. Mating type distribution, genetic diversity and population structure A. rabiei isolates from western Iran, using specific matting type primers, and ISSR and SSR molecular markers. Two mating types were identified, with the 57% of isolates belonging to MAT1-1. Ten ISSR markers produced 78 polymorphic bands with an average polymorphism information content (PIC) value of 0.33. Seven SSR markers showed high allelic variation (four to seven alleles) with the average PIC value of 0.61. The generated dendrogram using neighbor joining approach with ISSR and SSR marker data grouped isolates in three clusters. Combined dendrogram and model-based population structure analysis divided the isolates into two distinct populations. No significant correlation was found between geographical origins of isolates and their genetic diversity patterns, although the isolates from North Kermanshah and Kurdistan were closely grouped, and most of isolates from Lorestan and Kermanshah were clustered in a separate group. This relative spatial correlation between geographical locations and A. rabiei grouping indicated high genetic diversity within populations and no significant gene flow between distinctly geographical regions. This suggests the nece0ssity of continuous monitoring of A. rabiei populations in order to design effective chickpea breeding strategies to control the disease.
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