Letter | Published:

Signatures of adaptation in the weedy rice genome

Nature Genetics volume 49, pages 811814 (2017) | Download Citation

Abstract

Crop domestication provided the calories that fueled the rise of civilization1,2,3. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests4,5,6. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security. Here we use whole-genome sequences to examine the origin and adaptation of the two major strains of weedy rice found in the United States. We find that de-domestication from cultivated ancestors has had a major role in their evolution, with relatively few genetic changes required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. Genomic regions identified here that show evidence of selection can be considered candidates for future genetic and functional analyses for rice improvement.

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Acknowledgements

We thank M. Dyer and staff of the University greenhouse for assistance in growing plants and L. Small for technical laboratory assistance. We are grateful to members of the Olsen laboratory for helpful comments on this manuscript. This work is supported by the National Science Foundation Plant Genome Research Program (IOS-1032023). The USDA is an equal opportunity provider and employer.

Author information

Affiliations

  1. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.

    • Lin-Feng Li
  2. Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.

    • Lin-Feng Li
    •  & Kenneth M Olsen
  3. Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.

    • Ya-Ling Li
  4. US Department of Agriculture–Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA.

    • Yulin Jia
  5. Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA.

    • Ana L Caicedo

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Contributions

K.M.O., Y.J. and A.L.C. designed the experiments. L.-F.L. and Y.-L.L. analyzed the data. L.-F.L., K.M.O. and A.L.C. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ana L Caicedo or Kenneth M Olsen.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–16 and Supplementary Tables 2, 4–6 and 14

Excel files

  1. 1.

    Supplementary Table 1

    The list of 183 accessions of wild, cultivated, and weedy rice species sampled in the collection.

  2. 2.

    Supplementary Table 3

    Genetic assignments at wild, cultivated, and weedy rice accessions from two to five.

  3. 3.

    Supplementary Table 7

    Causative mutations of domestication genes in the three types of weedy rice.

  4. 4.

    Supplementary Table 8

    Genome-wide detection of regions of low nucleotide diversity in SH compared to indica.

  5. 5.

    Supplementary Table 9

    Genome-wide detection of regions of low nucleotide diversity in BHA compared to aus.

  6. 6.

    Supplementary Table 10

    Functionally characterized genes showing low nucleotide diversity in SH and high genetic differentiation between SH and indica.

  7. 7.

    Supplementary Table 11

    Functionally characterized genes showing low nucleotide diversity in BHA and high genetic differentiation between BHA and aus.

  8. 8.

    Supplementary Table 12

    Number of raw variants in wild, cultivated, and weedy rice with different filter criteria.

  9. 9.

    Supplementary Table 13

    Genome-wide detection and functional annotation of selective sweep regions in the full crop populations.

Text files

  1. 1.

    Supplementary Data

    Sequence alignment of Rc genes in wild, cultivated, and weedy rice.

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DOI

https://doi.org/10.1038/ng.3825

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