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Etude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques

Abstract : Yam (Dioscorea spp) is a major staple for more than 100 million people in Africa. The main objectives of the present PhD project were to study yam genomic diversity, its domestication, and to characterize the genomic determinism of its adaptation to different climatic zones. We investigated the genetic basis of yam domestication in a comparative genomic approach between the cultivated species D. rotundata and two wild close relatives D. praehensilis and D. abyssinica, by exploiting NGS sequencing data. We demonstrated that genes from the starch biosynthesis were selected during yam domestication. Genes related to tuber morphology or phototropism ability, as well as genes of the NADH dehydrogenase complex were also under selection. The same NADH-DH complex was also identified when assessing adaptation to climate variability. We also created the first de novo database of yam transposable elements (TEs). The study we performed on these repeat elements (REs) highlighted a strong correlation between the variability in relative abundances of numerous REs and climatic variability. Finally, we were able to propose an hypothesis on the origin of the cultivated yam D. rotundata. Our hypothesis identifies the origin of yam in the forest areas, with the species D. praehensilis as the putative progenitor. Our results question the generally admitted hypothesis of savannah origins for crops and agriculture in Africa.
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Roland Akakpo. Etude de la domestication et de l’adaptation de l’igname (Dioscorea spp) en Afrique par des approches génomiques. Bio-Informatique, Biologie Systémique [q-bio.QM]. Université Paris Saclay (COmUE), 2018. Français. ⟨NNT : 2018SACLS124⟩. ⟨tel-02925512⟩

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