SSR-Based Molecular Identification and Population Structure Analysis for the Yunrui-Series Sugarcane ( Saccharum spp . Hybrids) Genotypes

The success of sugarcane breeding depends on the understanding and exploitation of new germplasm. Sugarcane breeders often choose parental clones based on phenotypes when genotypes are unknown. In this study, an SSR fingerprint profile of 104 Yunrui-series sugarcane genotypes was constructed and the genetic diversity and population structure of these genotypes were analyzed using 21 pairs of fluorescence-labeled highly polymorphic SSR markers and a capillary electrophoresis platform. One hundred and thirty-six SSR fragments were detected. The percentage of polymorphic loci averaged 98.25%, and the polymorphism information content averaged 0.88. A neighbor-joining dendrogram and population structure analysis divided the 104 genotypes into four populations with a Q value of < 0.6 for half of the genotypes. Pairwise genetic differentiation ( Fst ) between populations ranged from 0.009 to 0.023. Analysis of molecular variance (AMOVA) revealed that 98% of the variations occurred within the populations, with a significant Fst value of 0.018 ( p < 0.001). The results demonstrated that Yunrui-series sugarcane genotypes shared a moderate to high level of genetic diversity, but a low level of genetic differentiation due to multiple occurrences of crossing and backcrossing involving a limited number of parents. Therefore, sugarcane breeders should consider the genetic distance and population structure information more than phenotype performance when choosing parental genotypes for crossing programs.