Genetic variation and population structure of Rosa roxburghii by EST-based and genomic SSR markers

摘要

Rosa roxburghii Tratt. is a well-known commercial horticultural plant in China with medicinal and nutritional values. The wild germplasm of this rose species is distributed mainly in southwest China, but the population is decreasing due to continuous exploitation, habitat destruction, and fragmentation. Therefore, assessing its genetic variation and population structure is important for effective conservation. In this study, 494 individuals from 29 natural populations from southwest China were analyzed using 10 EST-SSRs and 10 genomic-SSRs primer pairs. One hundred and fourteen different alleles were detected, with an average of 4.1 (for EST-SSR) and 7.3 (for Genomic-SSR) alleles per locus. The overall expected and observed heterozygosity values were 0.728 and 0.852, respectively, and the Shannon’s information index for each of the loci was 1.532. Our results revealed that genomic SSR markers were more polymorphic than EST-SSR markers. A moderately high level of genetic variation was maintained in the R. roxburghii population in Southwest China. AMOVA analyses showed that 93.10% of the genetic variation occurred within populations. Among the populations, the gene flow estimate of 3.373 had a high value. These R. roxburghii accessions were classified into two clusters, which did not follow the geographical distribution. Population ZJ, which showed the highest level of genetic variation and displayed a highly mixed genetic structure, was the most suitable for protection by an in situ conservation strategy.