Whole-genome duplication as a key factor in crop domestication

  • Nature Plants 2, Article number: 16115 (2016)
  • doi:10.1038/nplants.2016.115
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Polyploidy is commonly thought to be associated with the domestication process because of its concurrence with agriculturally favourable traits and because it is widespread among the major plant crops1,​2,​3,​4. Furthermore, the genetic consequences of polyploidy5,​6,​7 might have increased the adaptive plasticity of those plants, enabling successful domestication6,​7,​8. Nevertheless, a detailed phylogenetic analysis regarding the association of polyploidy with the domestication process, and the temporal order of these distinct events, has been lacking3. Here, we have gathered a comprehensive data set including dozens of genera, each containing one or more major crop species and for which sufficient sequence and chromosome number data exist. Using probabilistic inference of ploidy levels conducted within a phylogenetic framework, we have examined the incidence of polyploidization events within each genus. We found that domesticated plants have gone through more polyploidy events than their wild relatives, with monocots exhibiting the most profound difference: 54% of the crops are polyploids versus 40% of the wild species. We then examined whether the preponderance of polyploidy among crop species is the result of two, non-mutually-exclusive hypotheses: (1) polyploidy followed by domestication, and (2) domestication followed by polyploidy. We found support for the first hypothesis, whereby polyploid species were more likely to be domesticated than their wild relatives, suggesting that the genetic consequences of polyploidy have conferred genetic preconditions for successful domestication on many of these plants.

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We thank A. A. Levy and A. Rice for helpful discussions and suggestions. This study was supported by a post-doctoral fellowship to N.S. from the Edmond J. Safra postdoctoral fellowship and the Israel Science Foundation (1265/12) to I.M.

Author information

Author notes

    • Ayelet Salman-Minkov
    •  & Niv Sabath

    These authors contributed equally to this work.


  1. Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel

    • Ayelet Salman-Minkov
    • , Niv Sabath
    •  & Itay Mayrose


  1. Search for Ayelet Salman-Minkov in:

  2. Search for Niv Sabath in:

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The authors contributed in the following ways: conceptualization, I.M.; methodology, A.S.-M., N.S. and I.M.; software, N.S.; validation, A.S.-M. and I.M.; formal analysis, A.S.-M. and N.S.; investigation, A.S.-M. and N.S.; writing, A.S.-M., N.S. and I.M.; supervision, I.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Itay Mayrose.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Methods, Supplementary Figure 1, Supplementary Tables 1 and 2, Supplementary References

  2. 2.

    Supplementary Figure 2

    Inference of the temporal order of polyploidy and domestication events for all genera

Excel files

  1. 1.

    Supplementary Table 3

    Table of crop species by FAO commodity groups

  2. 2.

    Supplementary Table 4

    Table of loci used for each genus in reconstructing the phylogenetic trees

  3. 3.

    Supplementary Table 5

    Table of species names and categories

Zip files

  1. 1.

    Supplementary Data

    MSAs - The multiple sequence alignments for each genus. Trees - The set of bayesian phylogenetic trees reconstructed for each genus. analysis_script.R - This R script executes the temporal order of polyploidy and domestication analysis. Fragaria.RData - This is an RData file that contains the data for the genus Fragaria for example. It can be used for running the R script "analysis_script.R"