Identification, Genetic Diversity and Population Substructure in Cassava Using RAD Sequencing

Despite the economic importance of cassava, studies of diversity, population structure, and domestication have been limited, and have not been performed at whole genome level. In this study, we addressed these issues using RAD-seq to discover more than 500.000 genome-wide SNP genetic markers for over 450 cassava accessions from the International Center for Tropical Agriculture (CIAT) germplasm collection, and a wide representation of wild relative species of the genus Manihot. Preliminary results from  cassava accessions using 11,480 newly discovered SNPs revealed a complex pattern of population structure and clustered into five main subpopulations, without correlation to their geographical distribution. Differentiation between subpopulations was low to moderate, suggesting recent divergence and possible genetic flow between subpopulations. In addition, using 5,137 SNPs we could find a strong differentiation between cassava and wild relative species. Based on genetic differences, we traced the closest relatives of Cassava, and the genetic relationships among the different cultivars worldwide. Genetic diversity in cassava was found low compared with previous studies, and higher within the wild Manihot species. Finally, we selected the most informative SNPs, and generated a core set of SNPs suited for the unique identification of each one of the studied accessions. We used the Fluidigm SNPtype chip technology to validate the assays, and to corroborate the power of the core set of SNPs for fingerprinting identification. Overall, this genome wide approach allowed for high resolution population analysis, and when integrated with phenotype data, it will be useful for understanding the genetic bases of important agronomic traits.