Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10–25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and “Bulu” type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.

了解作物遗传多样性以及伴随其全球传播的进化过程对于设计有效的育种策略很有用。马达加斯加岛是旧世界最后的主要人类定居区之一，引入了水稻。对该岛的早期研究报告了马达加斯加特有的水稻群体的存在。使用 24 K SNP，我们比较了 620 个马达加斯加水稻和 1929 个亚洲水稻品种的全基因组和单倍型（基因组中 30 个 SNP 长片段）水平的多样性模式。单倍型水平分析旨在使用依赖于主成分分析特征空间中的核密度估计的组分配方法来识别相对于整个基因组水平的局部基因型变异。迁徙瓶颈导致马达加斯加籼稻和粳稻种群的多样性减少了 10-25% 。与亚洲同类相比，它们表现出的籼稻和粳稻基因渗入略低，表明这两个种群在迁徙到该岛时经历的重组较少。马达加斯加籼稻和粳稻群体的起源分别被描述为来自印度次大陆的籼稻亚群和来自马来群岛的热带粳稻。马达加斯加特有群体（Gm）具有相当高的基因多样性和原始的单倍型模式：与籼稻相比，籼稻单倍型的比例要低得多，而澳大利亚和粳稻单倍型的比例要高得多。它的出现和扩张很可能是由于马达加斯加中部高原的籼稻-澳大利亚混种和粳稻“Bulu”型地方品种之间的同源性促进的群体间重组，以及人类为适应低地水稻种植而进行的选择。水稻遗传多样性的模式也与岛上人类定居的历史密切相关。Gm群体的出现与最新抵达的南岛人有关，他们在高原上建立了梅里纳王国，并发展了低地水稻种植。作为水稻驯化三大支柱——澳大利亚、籼稻和粳稻之间的中间形式，转基因在热带高地耐寒育种中代表着非常有价值的遗传资源。我们为这个新的稻米组提议命名为Rojo。