A comprehensive map of rice genome variation has been constructed by sequencing 446 wild rice (Oryza rufipogon) accessions and 1,083 cultivated rice (Oryza sativa) varieties. This study identified 55 selective sweeps associated with rice domestication, revealing that O. sativa japonica was first domesticated from a specific population of O. rufipogon in southern China, while O. sativa indica was developed through crosses between japonica rice and local wild rice as the initial cultivars spread into Southeast and South Asia. The domestication-associated traits were analyzed through high-resolution genetic mapping, providing a valuable resource for rice breeding and an effective genomics approach for crop domestication research. The study also analyzed the genetic diversity and population structure of O. rufipogon, identifying three main groups (Or-I, Or-II, Or-III) that correspond to geographic distribution. The population differentiation (FST) among O. rufipogon groups was lower than that among O. sativa, indicating a more recent divergence. The study found that many domestication-related genes, such as Bh4, PROG1, sh4, qSW5, and OsC1, were among the 55 loci identified in the full population. These genes are associated with traits like hull color, tiller angle, seed shattering, grain width, and leaf sheath color. The study also identified 60 loci in indica, 62 in japonica, and 55 in the full population, with many showing strong selection signals. The domestication sweeps overlapped with characterized domestication-related QTLs, and the study found that the genetic diversity of O. rufipogon was higher than that of O. sativa, suggesting that O. rufipogon is likely the ancestral progenitor of O. sativa. The study also identified 213,188 indica-japonica-differentiated SNPs, with the differences in allele frequency attributed to the domestication bottleneck and the genetic diversity of the progenitor. The study further identified domestication-associated variants, including 128,010 non-synonymous SNPs and 49,236 sequence variants with large effects. The study also identified 305 sequence variants in the promoter regions with differential frequency between cultivated and wild rice, and 1,120 functional variants fixed in either japonica or indica panels. The study provided insights into the genetic basis of rice domestication, including the selection of chromosomal loci and the identification of domestication-associated genes. The study also highlighted the importance of wild rice populations in breeding efforts, as they contain more natural allelic variation than domesticated rice. The study's findings will help guide future breeding efforts and further understanding of rice domestication history.A comprehensive map of rice genome variation has been constructed by sequencing 446 wild rice (Oryza rufipogon) accessions and 1,083 cultivated rice (Oryza sativa) varieties. This study identified 55 selective sweeps associated with rice domestication, revealing that O. sativa japonica was first domesticated from a specific population of O. rufipogon in southern China, while O. sativa indica was developed through crosses between japonica rice and local wild rice as the initial cultivars spread into Southeast and South Asia. The domestication-associated traits were analyzed through high-resolution genetic mapping, providing a valuable resource for rice breeding and an effective genomics approach for crop domestication research. The study also analyzed the genetic diversity and population structure of O. rufipogon, identifying three main groups (Or-I, Or-II, Or-III) that correspond to geographic distribution. The population differentiation (FST) among O. rufipogon groups was lower than that among O. sativa, indicating a more recent divergence. The study found that many domestication-related genes, such as Bh4, PROG1, sh4, qSW5, and OsC1, were among the 55 loci identified in the full population. These genes are associated with traits like hull color, tiller angle, seed shattering, grain width, and leaf sheath color. The study also identified 60 loci in indica, 62 in japonica, and 55 in the full population, with many showing strong selection signals. The domestication sweeps overlapped with characterized domestication-related QTLs, and the study found that the genetic diversity of O. rufipogon was higher than that of O. sativa, suggesting that O. rufipogon is likely the ancestral progenitor of O. sativa. The study also identified 213,188 indica-japonica-differentiated SNPs, with the differences in allele frequency attributed to the domestication bottleneck and the genetic diversity of the progenitor. The study further identified domestication-associated variants, including 128,010 non-synonymous SNPs and 49,236 sequence variants with large effects. The study also identified 305 sequence variants in the promoter regions with differential frequency between cultivated and wild rice, and 1,120 functional variants fixed in either japonica or indica panels. The study provided insights into the genetic basis of rice domestication, including the selection of chromosomal loci and the identification of domestication-associated genes. The study also highlighted the importance of wild rice populations in breeding efforts, as they contain more natural allelic variation than domesticated rice. The study's findings will help guide future breeding efforts and further understanding of rice domestication history.