Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry

Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting species native to China. Simple sequence repeats (SSRs)—due their codominance, polymorphism, and stability—have been widely applied in genetic identification trait-association analysis. In this study, using comparative genomics strategy the data of one high-quality whole genome seven preliminarily assembled sequences, we constructed a database containing 25,779 polymorphic SSR loci efficiently develop novel markers. Sixty-four covering eight linkage groups were selected design primer pairs. Sixty (93.75%) pairs yielded specific bands 32 (50.00%) exhibited moderate-to-high levels informativeness (PIC ranging from 0.264 0.728) 94 accessions. A total 38 high transferability across 13 Cerasus taxa. The marker SAUCps203 was species-specific C. by checking with 114 accessions 16 relatives, suggesting its potential application accurate or interspecific hybrid. Moreover, 1081 out 1122 individuals three cross F1 populations identified as true hybrid offspring only five Trait association analysis suggested that 20 significantly associated soluble solids fruit size, explained phenotypic variance 9.02% 26.35%. This study will provide basis for SSR-based germplasm further marker-assisted selection (MAS) cherry.