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Demography and its effects on genomic variation in crop domestication

Nature Plants volume 4, pages 512–520 (2018)Cite this article

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Abstract

Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.

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Fig. 1: Features of demography and selection during plant domestication.
Fig. 2: The effects of demography on deleterious variants.
Fig. 3: The fitness effects of domestication and clonal propagation.
Fig. 4: SVs in populations and an example of an affected phenotype.

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Acknowledgements

The authors thank two anonymous reviewers, A. Muyle, E. Solares and T. Batarseh for comments. BSG is supported by NSF grants 1741627 and 1655808. DKS is supported by an NSF Postdoctoral Research Fellowship in Biology (1609024). QL is supported by the National Natural Science Foundation of China (grant no. 31471431) and the Training Program for Outstanding Young Talents of Zhejiang A&F University. YZ is supported by Y.Z. is supported by the International Postdoctoral Exchange Fellowship Program, China.

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  1. Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA

    Brandon S. Gaut, Danelle K. Seymour & Yongfeng Zhou

  2. College of Agriculture and Food Science, Zhejiang A&F University, Lin’an, Hangzhou, China

    Qingpo Liu

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Gaut, B.S., Seymour, D.K., Liu, Q. et al. Demography and its effects on genomic variation in crop domestication. Nature Plants 4, 512–520 (2018). https://doi.org/10.1038/s41477-018-0210-1

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  • DOI: https://doi.org/10.1038/s41477-018-0210-1

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