Rice Domestication Study

Characterization of rice genome variation is a foundation for understanding the relationship between genetic variation and agronomic traits, and for investigating origins of cultivated rice (Oryza sativa). Here we provide a comprehensive map of rice genome variation from sequencing of 446 geographically diverse accessions of wild rice species (Oryza rufipogon), which is the immediate progenitor of cultivated rice, and 1,083 varieties of cultivated indica and japonica rice. This map enables to reveal that the japonica rice was firstly domesticated from a small population of O.rufipogon within the region of Guangxi province of the Southern China, and the indica rice was subsequently developed from cross hybridizations between the japonica cultivars and other O.rufipogon groups as spreading of cultivated rice from China into Southeast and South Asia. We further identify 55 selective sweeps during domestication. The traits associated with the loci are assayed through a high-resolution mapping of a cross population between O. rufipogon and O. sativa. The genome of O. rufipogon accession W1943 is deeply sequenced and de novo assembled for detecting all functional variants. We therefore compare allele frequencies of the variants in cultivated and wild rice, and identify 273 domestication-related genes, including most well-characterized domestication genes. This study provides an important resource and an effective genomics approach for crop domestication research and rice breeding.