This study provides a comprehensive map of rice genome variation by sequencing 446 wild rice accessions and 1,083 cultivated rice varieties. The researchers identified 55 selective sweeps that occurred during domestication, revealing that Oryza sativa japonica rice was first domesticated from a specific population of Oryza rufipogon in southern China around the middle area of the Pearl River, 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 study also analyzed the genetic patterns around well-characterized domestication loci and identified 128,010 non-synonymous SNPs and 49,236 sequence variants with large effects. These findings provide insights into the evolutionary history of rice domestication and facilitate genetic mapping of complex traits in rice.This study provides a comprehensive map of rice genome variation by sequencing 446 wild rice accessions and 1,083 cultivated rice varieties. The researchers identified 55 selective sweeps that occurred during domestication, revealing that Oryza sativa japonica rice was first domesticated from a specific population of Oryza rufipogon in southern China around the middle area of the Pearl River, 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 study also analyzed the genetic patterns around well-characterized domestication loci and identified 128,010 non-synonymous SNPs and 49,236 sequence variants with large effects. These findings provide insights into the evolutionary history of rice domestication and facilitate genetic mapping of complex traits in rice.