Domesticated rice (Oryza sativa L.) accompanied the dawn of Asian civilisation and has become one of world's most important staple crops. Although O. sativa is genetically differentiated into several groups with limited crossability, it is generally accepted that the genealogical history of at least some parts of rice genome trace back to a single domestication process. This is indicated by allelic uniformity of several O. sativa genes considered to be crucial for the domestication phenotype. However, whether these alleles originated in the wild population or during cultivation – a critical question for the interpretation of the domestication process – remains unclear.
We conducted a multi-layer analysis of a published whole-genome dataset of wild and cultivated rice, including reconstruction of complete chloroplast genomes, comparison of genome-wide selective sweep patterns, quantification of shared derived variants, as well as examination of the diversity associated with the domestication genes. Analyses of the chloroplast haplotypes and selective sweep patterns confirm the general distinctiveness of the indica, japonica and aus groups, and quantification of shared derived variants fails to support a domestication model where crucial alleles spread across groups by introgressive hybridization. We also found that domestication alleles such as rc and laba1 (previously assumed to have emerged under cultivation) do occur in wild populations where they display higher associated diversity, indicating their pre-domestication origins.
All acquired evidence is consistent with geographically separate and genetically independent domestications leading to indica, japonica and aus rice. Given the presence of the sh4, prog1, rc and laba1 alleles in wild populations, their allelic uniformity in O. sativa is parsimoniously explained by parallel selection of closely related haplotypes from standing variation of O. rufipogon. Domestication of rice was therefore a multiregional process that did not depend on transcontinental cultural interaction and probably followed different dynamics in various parts of Asia.