Genetic Diversity of a Saccharum Core Collection Using Microsatellite Markers Derived Candidate Cold Tolerance Genes

Sugarcane, for its high biomass, is recognized as a viable feedstock for bioenergy industry. Cold tolerant high-biomass sugarcane (energy cane) varieties will expand their acreage beyond traditional sugarcane belts. Variations for cold tolerance exist in sugarcane primary and/or secondary gene pool. Cold tolerance genes/alleles and the linked molecular markers would be valuable for marker-assisted breeding of cold tolerant energy cane. Candidate genes-based markers may have higher linkage disequilibrium with the desired phenotype. To this end, publicly available cold tolerance genes were mined for SSR motifs and 100 SSR markers were used to genotype a core collection of 190 clones that comprised of 96 Louisiana commercial hybrids, S. spontaneum, Saccharum sp., S. officinarum, S. erianthus, S. bengalense, S. robustum, Miscanthus, S. arundinaceum, S. kanashiroi, two S. ravennae, S. rufipilum, S. coix, S. imperata, S. edule and S. barberi. A total of 1,377 alleles were detected by 67 polymorphic SSRs with 37.8 and 27.8 as the average and effective number of alleles, respectively. Polymorphic information content ranged from 0.005 to 0.484 with a mean of 0.211. The clones were grouped into 5 clusters with Louisiana hybrids in a separate cluster and S. sp. clones distributed among other species.  Louisiana clones had the highest number of unique alleles (51 of 99). Analysis of molecular variance showed 19% and 81% variation among and within populations, respectively. Genetic identity between populations was 0.900–0.984. Ongoing studies are focused to elucidate the role of variation in microsatellite loci in discriminating clones with varied cold tolerance.