Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers

Abstract

The genetic diversity and relationships among populations of Chinese-endemic rugged rose (Rosa rugosa) were studied at the molecular level, to provide theoretical guidance and technical support for the scientific evaluation, preservation and development of the germplasm resources of this endangered species. DNA samples of 120 specimens of R. rugosa, originating from six different Chinese source populations were amplified with CDDP (conserved DNA-derived polymorphism) primers. A total of 121 polymorphic loci out of the 128 total bands (94.53%) were recovered using 13 informative and reliable primers. The average number of amplified bands per primer was about 9.84. The number of specific bands was 8, accounting for 6.25%. Nei's gene diversity (H), Shannon's information index (I) and the effective number of alleles (Ne) were 0.3057, 0.4646 and 1.5131, respectively. A UPGMA (unweighted pair group method with arithmetic mean) cluster analysis suggested that these populations of rugged rose could be divided into six major groups, with a similarity coefficient of 0.81. Here we show that the CDDP marker technique can effectively reveal the genetic diversity among Chinese-endemic populations of the rugged rose. Based on the results from the cluster analysis, we suggest that although the population genetic structure mirrors the geographic structure to some extent, it is clear that other factors besides geographic distance contribute to the generation of genetic variation.