Rice domestication occurred through single origin and multiple introgressions

To the Editor -Rice domestication has long been a hot topic.Civáň et al. 1 recently suggested that the Asian rice varieties indica, aus and japonica were domesticated independently in different parts of Asia.They reanalysed previously published genomic data to ascertain the loci under selection in indica, aus and japonica, and identified 38 co-located low-diversity genomic regions (CLDGRs) by applying the π (wild) /π (domesticated) threshold of 4 for indica, aus and japonica separately.In 25 CLDGR trees, indica and japonica branched separately, leading to the conclusion that the three groups were domesticated independently.We argue that the methodology Civáň et al. used to identify domestication loci is technically flawed.We have previously sequenced the genomes of 1,083 accessions of cultivated rice (Oryza sativa) and 446 accessions of wild rice (Oryza rufipogon) 2 .Analysing these data, we showed that indica and japonica descend from different subpopulations of wild rice, namely Or-I and Or-IIIa, respectively.We identified the domestication loci, of which the validity was confirmed by the identification of quantitative trait loci (QTLs) for domestication traits.We further found that, unlike the genomewide pattern, the two subspecies were often clustered together at the domestication loci.Integrating all the data, we proposed a demographic scenario in which japonica was first domesticated from Or-IIIa, whereas indica was subsequently developed from Or-I with the adoption of many domestication alleles from japonica.We noticed that the domestication loci reported by Civáň et al. were mostly different from the domestication sweeps we had previously identified.The wellcharacterized domestication genes (such as An1, Bh4 and OsC1) [3][4][5] were located in our previous 55 domestication sweeps, but were not included in the 38 CLDGRs of