Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

Despite extensive studies on cultivated rice, the genetic structure and subdivision ofthis crop remain unclear at both global and local scales. Using 84 nuclear simple sequencerepeat markers, we genotyped a panel of 153 global rice cultivars covering all previouslyrecognized groups and 826 cultivars representing the diversity of Chinese rice germplasm.On the basis of model-based grouping, neighbour-joining tree and principal coordinateanalysis, we confirmed the widely accepted five major groups of rice cultivars(indica, aus, aromatic, temperate japonica andtropical japonica), and demonstrated that rayada rice was unique ingenealogy and should be treated as a new (the sixth) major group of rice germplasm. Withreference to the global classification of rice cultivars, we identified three major groups(indica, temperate japonica and tropical japonica) in Chineserice germplasm and showed that Chinese temperate japonica contained higherdiversity than that of global samples, whereas Chinese indica and tropicaljaponica maintained slightly lower diversity than that present in the globalsamples. Particularly, we observed that all seasonal, drought-tolerant and endosperm typesoccurred within each of three major groups of Chinese cultivars, which does not supportprevious claims that seasonal differentiation exists in Indica anddrought-tolerant differentiation is present in Japonica. It is most likely thatdifferentiation of cultivar types arose multiple times stemming from artificial selectionfor adaptation to local environments.