Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes

Microsatellites or simple sequence repeats (SSRs) markers are very informative for various applications in genetics and breeding. Information obtained with these markers has contributed to a better understanding of evolution and the complexity of the sugarcane genome. With the objective of identifying a large set of polymorphic microsatellite markers designated as Unigene derived Sugarcane Microsatellite (UGSM) and Sugarcane Enriched Genomic Microsatellite (SEGMS), 351 UGSM and 36 SEGMS were tested to find out informative SSRs marker for sugar content. These markers were screened and validated for their use in genetic diversity, cross transferability and comparative linkage potential in high and low sugar bulk of two segregating progenies and twenty each, cultivated high and low sugar cultivars. 158 (40.83%) of the microsatellite markers (144-UGSM: 14-SEGMS) were found to be highly robust and polymorphic. Cross amplification was estimated among nineteen accessions of six sugarcane cultivars, one inter specific hybrids, five related species, four related genera, and three divergent genera by using 27 UGSM primers. Analysis of 388 alleles, amplified by these markers, indicated the high number of observed allele ranged from 2 to 26, with an average of 14.37 alleles detected per locus. High level of polymorphism detected by these markers among sugarcane species, genera and cultivars was 96.3%, while cross-transferability rate was 98.0% within Saccharum complex and 88.27% to cereals. Wide range of genetic diversity (0.33–0.79 with an average of 0.56) assayed with UGSM markers suggested their importance in various genotypic applications in sugarcane.