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.

尽管针对栽培水稻已开展了广泛的研究，但该作物的遗传结构与亚群分化在全球及区域尺度上仍未明确。本研究利用84个核简单序列重复（nuclear simple sequence repeat）标记，对153份涵盖所有已确认类群的全球水稻栽培品种集合，以及826份代表中国水稻种质资源多样性的栽培品种进行了基因分型。基于模型聚类分析、邻接树构建与主坐标分析，我们验证了学界广泛认可的5个水稻栽培品种主要类群（籼稻（indica）、奥斯稻（aus）、香稻（aromatic）、温带粳稻（temperate japonica）与热带粳稻（tropical japonica）），同时证实雷亚达水稻（rayada）具有独特的谱系特征，应被划分为第六个水稻种质资源主要类群。参照全球水稻栽培品种分类体系，我们在中国水稻种质资源中鉴定出3个主要类群（籼稻、温带粳稻与热带粳稻）；分析结果显示，中国温带粳稻的遗传多样性高于全球样本，而中国籼稻与热带粳稻的遗传多样性则略低于全球同类样本。尤为重要的是，我们观察到中国3个主要栽培类群中均涵盖了所有季型、耐旱类型及胚乳类型，这一结果不支持此前"籼稻存在季型分化、粳稻存在耐旱类型分化"的论断。栽培品种类群的分化大概率是多次独立起源于适应本地环境的人工选择。