SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries

Capillary electrophoresis-based molecular genotyping was conducted on 35 sugarcane cultivars (Saccharum spp. hybrids) and 5 clones of related wild species with 20 polymorphic SSR DNA markers. A total of 251 alleles were identified with 248 alleles displaying varying degrees of polymorphism and the remaining three alleles being monomorphic. The total number of alleles by any SSR marker varied from as few as 7 to as many as 18, with an average of 12.5 alleles per marker. Diversity index for these SSR markers ranged from 0.71 to 0.91, with a mean of 0.83. A composite parameter NDI, representing a product of the number of alleles (N) and DI, is an indicator on the general usefulness of a DNA marker. Ten SSR markers, namely, mSSCIR43, mSSCIR66, SMC119CG, SMC24DUQ, SMC278CS, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, and SMC851MS, have NDI values of greater than 12 in comparison to less than 10 from the rest markers, indicating that these 10 SSR markers provide much information for genotyping the 40 clones. A finding to minimize stutters and minus-Adenine peaks gave a guideline for the selection of best SSR markers for other SSR research. The 35 cultivars were clustered into five groups based on pairwise similarity coefficient values and their relationships to the wild species were demonstrated. Inclusion of CP67-412, CP72-1210, N21, N27, and S. officinarum clone Badila into the cultivar groups is due to the fact that these clones have been extensively used as parental material in sugarcane breeding programs. The results are in general agreement with the evolutionary course of the sugarcane cultivars that the order of contributing species in modern sugarcane cultivars is S. officinarum, S. spontaneum, S. robustum Brandes et. Jesw. ex., S. sinense Roxb., and S. barberi Jesweit. The accordance of molecular results with recorded evolution of sugarcane verified the fidelity and usefulness of these 20 SSR markers in progeny selection and allele transmission study in this aneu-polyploidy crop. © Society for Sugar Research & Promotion 2009.