Genetic diversity and population structure in cherry (Cerasus pseudocerasus (Lindl). G. Don) along Longmenshan Fault Zones in China with newly developed SSR markers

•20 Polymorphic SSR markers were developed from Cerasus. pseudocerasus genome and were used to estimate the genetic diversity and population structure of 15 natural populations from the Longmenshan Fault Zones.•Genetic diversity and population structure were comprehensively studied and discussed between wild and landrace populations.•The effects of uniquely geological history on the genetic diversity and differentiation of C. pseudocerasus were studied in this region.

Chinese cherry (Cerasus pseudocerasus (Lindl). G. Don), native to China, is a commercially valuable fruit crop with extensive morphological diversity along Longmenshan Fault Zones, a region adjacent to the Qinling and Hengduan Mountains. In this study, we developed simple sequence repeat (SSR) markers from its own genome to comprehensively investigate the genetic variation of Chinese cherry in this center which is well-known by frequent geological activities and high levels of biodiversity. A total of 33,263 microsatellite sites were identified from the C. pseudocerasus genome, among which 30,148 SSR markers were designed. Of these markers, two hundred primer pairs were evaluated, and finally 20 polymorphic markers were selected to assess the genetic diversity and population structure of 15 representative natural populations (214 total individuals) in the region. The results revealed a moderately high genetic diversity in C. pseudocerasus (Na = 7.00, He = 0.62, PIC = 0.59, I = 1.26). A reduction of genetic variation, heterozygote excess and domestication bottleneck were detected in landrace populations (Na = 4.00, He = 0.41, Ar = 1.87, FIS = −0.11) when compared with the wild ones (Na = 6.95, He = 0.65, Ar = 2.49, FIS = 0.35).The mantel test showed no significant correlation between geographic and genetic distance (r = 0.581, P = 0.08). Moderate differentiation and frequent gene flow were detected among all populations (FST = 0.0659, P = 0000, Nm = 3.5436). Nevertheless, a clear structure and relatively high differentiation (FST = 0.1173, P = 0000, Nm = 1.8813) were observed between most wild and landrace populations according to the STRUCTURE clustering and AMOVA analyses. The newly-developed SSR markers in our study exhibited high efficiency and can be utilized in further studies on this species and relatives. Meantime, the comprehensive assessments of genetic diversity of Chinese cherry resources in the biodiversity center have provided us basic genetic knowledge of this species, and this information will be very useful to policy makers on cherry breeding plan and species conservation.