ObjectiveThis research provides some information for the controversy over some taxonomy and phylogenetic problems on Rosa species, and provides basis for the selection of parents of interspecific hybrids. This will provide a theoretical basis for further development of abundant wild rose resources in China.

MethodIn this study, 50 samples with 42 species and varieties of genus Rosa were used to analyze genetic relationships and construct phylogenetic trees based on SSR markers and single copy nuclear gene (GAPDH). In order to predict the genotype of polyploidies, MAC-PR method was used.

ResultA total of 382 alleles were detected at 29 loci. The polymorphism information content ranged from 0.413 9 to 0.934 0 with an average value of 0.798 9. Then we calculated the Bruvo distance and constructed NJ tree (Neighbour-joining tree). The problem to apply SSR markers in polyploidies was solved in the above-mentioned territory. The phylogenetic tree based on GAPDH fragment was also constructed by Bayesian inference. The phylogenetic tree showed that 50 accessions could be clustered into 6 taxa. The traditional classification system of Chinenses and Synstylae is mostly supported by molecular data while others not. GAPDH sequence fragments from all accessions were successfully obtained after cloning and sequencing. The sequence length was 841 bp with 164 variable loci. The phylogenetic relationship based on GAPDH did not correspond to traditional classification system.

ConclusionThe result showed that the genus Rosa in its traditional infrageneric circumscription is not supported by molecular data. Sect. Chinenses and Sect. Synstylae are closed in genetic relationship. Sect. Pimpinellifoliae and Sect. Cinnamomeae are not monophyletic and a predicted gene flow exists between these sections. Two species in Sect. Microphyllae are not related based on molecular data.