Association analysis of flowering time and single nucleotide variations at Ppd-H1, HvCO1, and HvGI genes in barley(H.Vulgare)

In order to identify effective SNP markers of barley flowering time in candidate genes Ppd-H1, CO1, and GIGANTEA, association analysis was conducted in a set of 52 Iranian and non-Iranian barley cultivars. Based on 42 EST-SSRs the genetic structure of the population was divided to two subgroups corresponding to the origin of the cultivars. High nucleotide diversity was observed in the exon region of Ppd-H1 while CO1 and GIGANTEA showed limited diversity. Within all three genes, the extent of linkage disequilibrium (LD) was variable and low, indicating that the candidate gene association approach could be a reliable tool to reach a high resolution map for flowering time in barley. Significant associations were observed for GIGANTEA and Ppd-H1 with flowering time, causing one week difference in flowering time. While no significant association was seen between nucleotide diversity in intron region of the CO1 and flowering time. The haplotypes of 3 genes showed no significant intergenic interactions. Valuable nucleotide diversity in the the mentioned candidate genes was detected in the germplasm specially within Iranian cultivars that could be applied in breeding for flowering time in barley. Some identified SNP alleles accelerating the time of flowering for one week, were detected in this study capable of being used in marker assisted selection. A novel allele was also detected in the gene GIGANTEA with important role in late flowering.