Optimal use of SSRs for establishing genetic Relationships and variety identification in a collection of Sugarcane hybrids

Simple sequence repeat (SSR) analysis was carried out to assess genetic diversity and to establish genetic relatedness among sugarcane hybrids in a collection of 62 genotypes. Molecular data were also used to determine the discriminating power and utility of different SSR primers for sugarcane genotype identification and to find the optimal primer combination to ensure unambiguous identification. In 62 sugarcane hybrids, a total of 107 loci were detected with 13 SSR primers. The percentage of polymorphic loci was quite high (94%), with the NKS23, mSSCIR19 and NKS34 primers revealing the highest levels of polymorphism. The dissimilarity coefficients ranged from 0.064 to 0.68 with a mean of 0.46. The majority-rule consensus tree showed eight main clusters supported by more than 50% occurrences with several subgroups with the maximum bootstrap score (100%). A total of 315 banding patterns were detected. Discrimination power analysis revealed that the efficiency of a given primer does not depend only on the number of bands or the banding pattern but also on the frequency of differences between patterns generated by the primers. The primers NKS23 and mSSCIR19 generated patterns at the same frequency (isofrequencies) and have a maximal discriminating power. PIC values close to 1 (0.719 to 0.985) demonstrated that, in spite of the low number of primers, these SSR were sufficiently polymorphic, discriminating, and informative and will be useful in sugarcane variety registration and in genetic identity tests.