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

Despite extensive studies on cultivated rice, the genetic structure and
subdivision of this crop remain unclear at both global and local scales.
Using 84 nuclear simple sequence repeat markers, we genotyped a panel of
153 global rice cultivars covering all previously recognized groups and
826 cultivars representing the diversity of Chinese rice germplasm. On the
basis of model-based grouping, neighbour-joining tree and principal
coordinate analysis, we confirmed the widely accepted five major groups of
rice cultivars (indica, aus, aromatic, temperate japonica and tropical
japonica), and demonstrated that rayada rice was unique in genealogy and
should be treated as a new (the sixth) major group of rice germplasm. With
reference to the global classification of rice cultivars, we identified
three major groups (indica, temperate japonica and tropical japonica) in
Chinese rice germplasm and showed that Chinese temperate japonica
contained higher diversity than that of global samples, whereas Chinese
indica and tropical japonica maintained slightly lower diversity than that
present in the global samples. Particularly, we observed that all
seasonal, drought-tolerant and endosperm types occurred within each of
three major groups of Chinese cultivars, which does not support previous
claims that seasonal differentiation exists in Indica and drought-tolerant
differentiation is present in Japonica. It is most likely that
differentiation of cultivar types arose multiple times stemming from
artificial selection for adaptation to local environments.