Molecular Identification and Genetic Diversity Analysis of Chinese Sugarcane (Saccharum spp. Hybrids) Varieties using SSR Markers

Sugarcane (Saccharum spp. hybrids) is an important sugar and renewable bio-energy crop with a high aneu-polyploidy and complex genome. The complex characteristics of sugarcane genome enhance the difficulty of selecting elite varieties in sugarcane breeding program. The objectives of this study were to establish the molecular identities (ID) of 91 nationally or provincially released Chinese sugarcane varieties and to evaluate the extent of genetic diversity among these varieties using SSR DNA markers and two fingerprinting systems, i.e., capillary electrophoresis (CE) and polyacrylamide gel electrophoresis (PAGE). A total of 151 SSR alleles together with 20 new alleles were detected by CE and 117 SSR alleles were detected by PAGE. Primer pairs SMC336BS, SMC31CUQ, and SMC597CS amplified more than eight alleles detectable by either CE or PAGE. Polymorphism information content (PIC) values of the SSR markers varied from 0.71-0.98 with an average of 0.90 for CE, or from 0.55-0.95 with an average of 0.84 for PAGE. UPGMA method classified the 91 varieties based on the CE data into four major groups with pair-wise similarity coefficients ranging from 58% to 95%. The genetic similarity estimates within and between the four groups varied from 0.31 to 0.87, with a mean of 0.49. Our results illustrated that the 21 SSR primer pairs in combination with CE or PAGE detection system could be a very useful working tool for molecular identification of sugarcane varieties, genetic diversity assessment, and parental selection in sugarcane breeding.