Wild barley (Hordeum vulgare subsp. spontaneum), the progenitor of cultivated barley (Hordeum vulgare subsp. vulgare), is crucial for enhancing genetic diversity in breeding programs. The genetic diversity and structure of wild barley populations in western Iran are not well understood. This study evaluated 114 wild barley genotypes from four provinces in western Iran using SSR and EST-SSR markers. SSR markers revealed a considerable number of alleles, with an average of 2.7 per marker, while EST-SSR markers exhibited a slightly higher mean allele count of 2.8 per marker. Most genetic variation occurred within populations (97% for SSR and 98% for EST-SSR), with low differentiation among populations (Fst = 0.033 and 0.026). Various diversity indices were calculated, with SCSSR04163 showing the highest values. Jaccard coefficients revealed significant genetic distance among genotypes, especially between populations from different provinces. Cluster analysis categorized the genotypes into distinct groups based on SSR and EST-SSR markers. The Mantel test showed weak correlation (r = 0.10048, p = 0.9738) between the two dendrograms. Population structure analysis identified three optimal clusters (K = 3). This study demonstrates the utility of SSR and EST-SSR markers in understanding the genetic diversity and structure of wild barley, providing valuable insights for conservation and improvement.
