Abstract

Drought is one of the major environmental factors negatively affecting cultivated crop species. Thirty-one candidate genes for drought tolerance in barley were selected using a literature survey. SNP discovery was performed by aligning the corresponding nucleotide sequences of each candidate gene and SNPs with a base change from A/T to C/G or vice versa were selected. Primer pairs were designed to flank the selected SNPs. Using HRM analysis, all these markers showed polymorphism among 10 examined cultivars. The polymorphic information content (PIC) value of SNP markers ranged from 0.164 to 0.5, with a mean value of 0.307. Genetic diversity analysis of the HRM-SNPs data using UPGMA clustering grouped the studied barley cultivars into two clusters according to their drought tolerance. The first cluster encompassed the seven drought-tolerant cultivars and the second cluster contained drought-susceptible cultivars. In conclusion, HRM analysis is an effective method for SNPs genotyping and gene-based SNPs are particularly attractive for candidate gene-based association analyses, QTL mapping and functional diversity.