Crop domestications are long-term selection experiments that have greatly advanced human civilization. The
domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history.
However, its origins and domestication processes are controversial and have long been debated. Here we generate
genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the
immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct
a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps
that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns
reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the
middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from
crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The
domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an
important resource for rice breeding and an effective genomics approach for crop domestication research.