Study of Genetic Diversity and Population Structure in Barley (Hordeum vulgare L.) Based on SNP Markers

Barley is a major crop and the fourth most important cereal in the world. Genetic diversity is a basic component in breeding programs and is crucial for successful barley improvement. SNPs are a good marker type to study diversity. SNPs represent the most abundant source of genetic variation within the genome and are linked to heritable differences between individuals. in this study we used diverse collection of 100 winter barley (Hordeum vulgare L.) to assess genetic diversity and population structure. Population was genotyped using 3964 SNPs with minor allele frequencies (MAFs) more than 10 percent. PIC was ranged from 0.19 to 0.5 in the whole panel and it was more than 0.25 for 3352 markers. The average of PIC was varied from 0.37 (2H and 5H chromosomes) to 0.42 (3H and 7H chromosomes). strong population structure effect related to ear row number (two-row and six-row) was present in our barley collection. AMOVA analysis and Fst index showed that differentiated regions of genome are correspondence with ear row number loci. In the whole genome, average linkage disequilibrium (LD) was observed to decay at 4cM and in sub populations was more than whole panel. LD decay was more rapid in six-row cultivars compared to two-row. These results indicated considerable genetic variation in winter barley collection and could be used in barley improvement programs.