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. 2019 May 1;5(5):eaaw1947.
doi: 10.1126/sciadv.aaw1947. eCollection 2019 May.

Yam genomics supports West Africa as a major cradle of crop domestication

Nora Scarcelli  1 , Philippe Cubry  1 , Roland Akakpo  1 , Anne-Céline Thuillet  1 , Jude Obidiegwu  2 , Mohamed N Baco  3 , Emmanuel Otoo  4 , Bonaventure Sonké  5 , Alexandre Dansi  6 , Gustave Djedatin  6 , Cédric Mariac  1 , Marie Couderc  1 , Sandrine Causse  7   8 , Karine Alix  9 , Hâna Chaïr  7   8 , Olivier François  10 , Yves Vigouroux  1
Affiliations

Yam genomics supports West Africa as a major cradle of crop domestication

Nora Scarcelli et al. Sci Adv. .

Abstract

While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

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Figures

Fig. 1
Fig. 1. The three yam species analyzed in this study and corresponding sampling.
(A) Tuber of D. rotundata. (B) Tuber of D. abyssinica. (C) Tuber of D. praehensilis. (D) Map representing the geographical coordinates of each analyzed yam individual. Orange circle, D. rotundata; green triangle, D. abyssinica; blue square, D. praehensilis. Photo credits: Nora Scarcelli, IRD.
Fig. 2
Fig. 2. Genetic structure of the three species.
(A) PCA based on SNPs remaining after a 5% minimum allele frequency (MAF) cutoff. (B) Ancestry proportions of each sample estimated by admixture for K = 4 genetic groups. (C) Geographic distribution of ancestry proportions of wild population samples obtained from the same analysis. Orange, D. rotundata; green, D. abyssinica; dark blue, Western D. praehensilis; light blue, Cameroonian D. praehensilis.
Fig. 3
Fig. 3. Inference of African yam domestication history.
(A) Yam species relationship. The best model inferred by coalescent-based analysis is presented here. AIC, Akaike information criterion. (B) Inferred area of geographic origin of cultivated yam based on an approximate Bayesian spatial model. (C) Demographic history of cultivated yam populations (effective size, Ne). The three arrows represent the following: (i) the first expansion of yam agriculture, ca. 2500 generations ago; (ii) the second expansion, ca. 700 generations ago; and (iii) the recent decrease, ca. 400 generations ago. Orange, D. rotundata; green, D. abyssinica; dark blue, Western D. praehensilis; light blue, Cameroonian D. praehensilis.
Fig. 4
Fig. 4. Near East and West African major cradles of domestication.
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References

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