Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Multiple domestications of Asian rice

Nature Plants volume 2, Article number: 16037 (2016) Cite this article

Subjects

To the Editor — In their recent Correspondence1 about our study showing that there were three origins of Asian rice2, Huang and Han suggest that the methodology that we used to infer multiple domestications was flawed as it did not take account of the strong genetic bottleneck in japonica. We agree that the differences in diversity between japonica and the other groups present a challenge when comparisons are made, and we explored this issue in some detail in the Supplementary Information of our paper2.

Specifically, Huang and Han criticized our choice of a π(wild)/π(domesticated) threshold of 4 for each of japonica, indica and aus, and implied that a higher threshold would be more appropriate for the detection of selective sweeps in japonica. We did, in fact, test the data with such an approach —it is described in the first paragraph of the Methods section of the paper, and the resulting tree is presented as Supplementary Fig. 12. In brief, we compared the sweeps Huang et al.3 identified for indica at threshold 3 against the sweeps they identified for japonica at threshold 14 (Supplementary Section 2 of ref. 3) and extracted genomic regions that are detected as sweeps in both groups (‘sweep overlaps’). The resulting tree reveals that even when a much higher sweep threshold is used for japonica (to reduce the swept fraction of the japonica genome), indica, japonica and aus still form separate clusters. We are therefore confident that the strong japonica bottleneck does not influence our results in the way suggested by Huang and Han1.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

References

  1. Huang, X. & Han, B. Nature Plants 2, 15207 (2015).

    Article  Google Scholar 

  2. Civán, P., Craig, H., Cox, C. J. & Brown, T. A. Nature Plants 1, 15164 (2015).

    Article  Google Scholar 

  3. Huang, X. et al. Nature 490, 497–503 (2012).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, M1 7DN, UK

    Peter Civán, Hayley Craig & Terence A. Brown

  2. Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-139, Portugal

    Cymon J. Cox

Authors
  1. Peter Civán
    View author publications

    Search author on:PubMed Google Scholar

  2. Hayley Craig
    View author publications

    Search author on:PubMed Google Scholar

  3. Cymon J. Cox
    View author publications

    Search author on:PubMed Google Scholar

  4. Terence A. Brown
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Terence A. Brown.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Civán, P., Craig, H., Cox, C. et al. Multiple domestications of Asian rice. Nature Plants 2, 16037 (2016). https://doi.org/10.1038/nplants.2016.37

Download citation

  • Published:

  • DOI: https://doi.org/10.1038/nplants.2016.37

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing