Whole Genome Sequencing of Elite Rice Cultivars Reveals Recurrent Copy Number Variation, Diversity Patterns, and Variety Specific Introgression Events in Oryza sativa spp. japonica and indica

Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Comprehensive databases of variation among thousands of varieties will be released within the next years. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to produce significant improvements for development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 60 rice varieties belonging to the major subspecies of Oryza sativa (indica and japonica). We built a database of repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. We identified close to 1 million SNPs in unique and copy number neutral regions, from which about 100 thousand allow to differentiate indica and japonica cultivars. Over 20,000 SNPs show high minor allele frequency (MAF) within indica and over 10,000 SNPs showed high MAF within japonica. Window-based analysis of the genome revealed regions of high diversity and high conservation, and also variety specific indica-japonica introgressions. Combining gene ontologies, predicted sites of conservation, and observed non-synonymous variation, we identified several candidate genes with a high percentage of allele sharing associated with grain yield and quality, heading date, biotic and abiotic stress, and gene regulation. Selected non-synonymous SNPs on different genes of interest are currently under testing for marker assisted selection.