Genetic diversity in barley from west China based on RAPD and ISSR analysis

Two types of molecular markers, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were assayed to determine the genetic diversity of 46 barley accessions, including 27 landraces of H. vulgare ssp vulgare (HV), 6 accessions of H. vulgare ssp. spontaneum (HS) and 13 accessions of H. vulgare ssp. agriocrithon (HA), from west China. A high level of polymorphism was found with both RAPD and ISSR markers, and the mean polymorphism information content (PIC) values were 0.574 and 0.631 for RAPD and ISSR markers, respectively. In RAPD analyses, 84 out of 109 bands (77.06%) were polymorphic. The number of alleles ranged from 2 to 8 per primer, with an average of 4.19 per primer. The RAPD-based genetic similarity (RAPD-GS) ranged from 0.753 to 0.980, with the mean of 0.864. In ISSR analyses, a total of 107 alleles were detected, among which 105 alleles (98.13%) were polymorphic. The number of alleles per primer ranged from 2 to 10 with an average of 5.94 alleles per ISSR primer. The ISSR-derived genetic similarity (ISSR-GS) ranged from 0.212 to 0.931, with the mean of 0.674. ISSR was better than RAPD to detect genetic diversity among the barley accessions. A poor correlation (r = 0.113) was found between both sets of genetic similarity data, suggesting that both sets of markers revealed unrelated estimates of genetic relationships. Cluster analyses indicated that all 46 barley accessions could be distinguished by both RAPD and ISSR markers.