Worldwide Genetic Diversity of the Wild Species Saccharum spontaneum and Level of Diversity Captured within Sugarcane Breeding Programs

Sugarcane (Saccharum spp.) is grown in tropical and subtropical regions of the world and produces 80% of the world's sucrose primarily for human consumption but is increasingly used as a feedstock for biofuel. Commercial cultivars are hybrids between two species, Saccharum officinarum L. and S. spontaneum L. Saccharum spontaneum is the wild species with generally low sucrose levels and is used to introgress traits such as high yield, increased disease resistance, and ratooning. Molecular markers generated across the Saccharum genome were used to analyze diversity across 430 S. spontaneum accessions collected from 21 different countries and 255 cultivars from two breeding programs. A total of 724 markers were used for principle coordinate and cluster analysis, which revealed two main clusters that corresponded to accessions collected north or south of the Tropic of Cancer. The majority of the accessions clustered according to country of origin. Genetic similarity ranged from 0.25 to 0.54, with the highest diversity in accessions collected in Indonesia, followed by China, India, and Thailand, and the lowest in the Philippines. The diversity in the cultivar collection was lower than in the S. spontaneum accessions, as expected. Despite the low number of S. spontaneum clones used for breeding varieties, 51 to 80% of markers were captured in the breeding populations, although many at a low frequency. This is due to the high heterozygosity of sugarcane related to high ploidy and the introgression programs that have been performed in a number of sugarcane breeding programs. The genetic similarity was highest within the breeding program, and there remains large amounts of unexplored diversity in the wild germplasm. Diversity analysis could be used to guide the selection of wild S. spontaneum accessions, along with phenotypic data for introgression into breeding programs to increase genetic diversity.