Patterns of rice diversity from SNP delineated the origin of the atypical O. sativa group in Madagascar from intermediary forms of the Indian sub-continent

Madagascar Island was one of the last major Old World areas where human settlement was accompanied by the introduction of Oryza sativa. Early studies had reported the presence of a rice group specific to Madagascar. Using 1536 SNP markers, we compared diversity patterns between a panel of 147 Malagasy rice varieties, a reference panel of 370 Asian varieties and representatives of wild relatives of O. sativa. Migration bottleneck has resulted in 30-40% reduction of diversity among the indica and japonica groups in Madagascar. The Malagasy panel showed many fewer indica x japonica recombinations compared to the Asian panel, suggesting that the two groups had undergone much less recombinations when migration to the Island occurred. The existence of the Malagasy-specific group (Gm) was confirmed. Its diversity patterns positioned it halfway from indica and aus groups. Madagascar also hosted cold tolerant tropical japonica varieties, with very long grain. The Gm group most probably arose from founder effect from intermediary forms of rice originated from either India or Sri Lanka that did not belong to the four majors O. sativa groups. It then underwent human selection for cold tolerance. Signs of inter-group recombinations were also observed, but recombinations did not seem to have played a major role in the dynamics of rice adaptation to the Island's agro-ecological constraints. Connections between Gm and O. rufipogon from its putative area of origin reinforce the hypothesis of multiple and diffuse domestication of O. sativa as opposed to two independent domestications occurring in two distinct geographical areas. (Texte intégral)