A survey sequence comparison of saccharum genotypes reveals allelic diversity differences

Sugarcane (Saccharum spp.) is a crop of substantial international significance for both food and fuel, however its highly polyploid nature challenges investigation of its genetic composition. Efforts to generate the full sugarcane genome sequence are underway, however in the meantime crop improvement efforts are somewhat limited by the lack of genome sequence resources available for physiological characterization. Low-coverage survey sequence data was generated and assembled for six sugarcane genotypes representing a range of significant S. spontaneum, S. officinarum, and S. hybrid cultivar accessions from around the world. These data were explored to investigate the composition of repetitive sequences and variations in chloroplast genome sequence, as well as assembled into a conglomerate monoploid genome sequence for polymorphism comparison between the genotypes. Almost half (47 %) of the inter-genomic polymorphisms analysed in these data represented poly-allelic variations which cannot be applied in traditional present/absent marker analysis, suggesting that new approaches are required to better understand and access genetic diversity within the Saccharum genus. These results support previous assertions that S. spontaneum is both less repetitive (62 % repetitive k-mers in Mandalay vs. 65 % in IJ76-514) and more highly polymorphic (17 % poly-alleles in Mandalay vs. 10 % poly-alleles in IJ76-514) than S. officinarum, with S. hybrids being intermediate between the two. However, contrary to previous analysis the monoploid genome size of S. spontaneum does not appear to differ significantly from that of S. officinarum as had been expected. This genomic survey assembly will be a very useful resource for sugarcane genomics in the absence of a monoploid or polyploid genome sequence, and will be made available upon request.