Research ArticleAGRICULTURE

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

See allHide authors and affiliations

Science Advances  01 May 2019:
Vol. 5, no. 5, eaaw1947
DOI: 10.1126/sciadv.aaw1947
  • 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 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 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 Near East and West African major cradles of domestication.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/5/eaaw1947/DC1

    Fig. S1. Genetic diversity of yam samples.

    Fig. S2. Smoothed representation of the estimation of LD decay for each population.

    Fig. S3. Models tested using fastsimcoal.

    Fig. S4. Estimation of the geographical origin of cultivated yam.

    Fig. S5. Changes in the effective size (Ne) of wild populations.

    Fig. S6. Results of the selection tests along the 21 chromosomes of D. rotundata.

    Table S1. Field and genetics characteristics of the samples.

    Table S2. Nucleotide diversity calculated for each population defined at K = 4.

    Table S3. Annotations for genes corresponding to region under selection.

    Table S4. Fisher exact test on GO terms enrichment in genes detected under selection during the domestication process of yam.

  • Supplementary Materials

    The PDF file includes:

    • Fig. S1. Genetic diversity of yam samples.
    • Fig. S2. Smoothed representation of the estimation of LD decay for each population.
    • Fig. S3. Models tested using fastsimcoal.
    • Fig. S4. Estimation of the geographical origin of cultivated yam.
    • Fig. S5. Changes in the effective size (Ne) of wild populations.
    • Fig. S6. Results of the selection tests along the 21 chromosomes of D. rotundata.

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • Table S1 (Microsoft Excel format). Field and genetics characteristics of the samples.
    • Table S2 (Microsoft Excel format). Nucleotide diversity calculated for each population defined at K = 4.
    • Table S3 (Microsoft Excel format). Annotations for genes corresponding to region under selection.
    • Table S4 (Microsoft Excel format). Fisher exact test on GO terms enrichment in genes detected under selection during the domestication process of yam.

    Files in this Data Supplement:

Navigate This Article