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.

尽管针对栽培稻已开展了大量研究，但该作物在全球及区域尺度下的遗传结构与群体分化仍未明确。本研究利用84个核简单序列重复（nuclear simple sequence repeat）标记，对153份覆盖所有已报道类群的全球水稻品种集合，以及代表中国水稻种质资源多样性的826份中国水稻品种进行了基因分型。基于模型的群体分组分析、邻接系统发育树构建与主坐标分析，我们证实了学界普遍认可的五大水稻品种类群：籼稻（indica）、奥斯稻（aus）、香稻（aromatic）、温带粳稻（temperate japonica）与热带粳稻（tropical japonica），并发现雷亚达稻（rayada rice）在系统发育谱系中独具特色，应作为第六个全新的水稻种质资源主要类群进行划分。结合全球水稻品种分类体系，我们在中国水稻种质资源中鉴定出三大主要类群：籼稻、温带粳稻与热带粳稻；分析表明，中国温带粳稻的遗传多样性高于全球温带粳稻样本，而中国籼稻与热带粳稻的遗传多样性则略低于全球对应类群样本。尤为值得注意的是，我们发现中国三大水稻类群中均涵盖了所有季节适应性类型、耐旱性类型与胚乳类型，这一结果不支持此前“籼稻存在季节分化、粳稻存在耐旱性分化”的学术观点。水稻品种类群的分化大概率经历了多次独立起源过程，其驱动因素为适应本地环境的人工选择。