Abstract

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa 3,000 years ago1,2,3. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses4,5. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began 13,000–15,000 years ago with effective population size reaching its minimum value 3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within 300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.

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Acknowledgements

We would like to thank E. Septiningsih for critical discussions. We are grateful to M. Sock and B. Fonton for field assistance, to International Rice Research Institute staff for phenotyping assistance, and to J. Maritz and Z. Joly-Lopez for laboratory assistance. We thank the US Department of Agriculture and International Rice Research Institute for providing germplasm. This work was funded in part by grants from the National Science Foundation Plant Genome Research Program (IOS-1126971), the Zegar Family Foundation and the New York University Abu Dhabi Research Institute to M.D.P., as well as by a National Science Foundation Plant Genome Postdoctoral Fellowship (IOS-1202803) to R.S.M.

Author information

Affiliations

  1. Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.

    • Rachel S Meyer
    • , Jae Young Choi
    • , Michelle Sanches
    • , Anne Plessis
    • , Jonathan M Flowers
    • , Katherine Dorph
    •  & Michael D Purugganan
  2. Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.

    • Rachel S Meyer
    • , Jonathan M Flowers
    • , Khaled M Hazzouri
    •  & Michael D Purugganan
  3. Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.

    • Junrey Amas
    • , Annie Barretto
    •  & Glenn B Gregorio
  4. Department of Biology, University of Minnesota, Duluth, Minnesota, USA.

    • Briana Gross
  5. Institute of Archaeology, University College London, London, UK.

    • Dorian Q Fuller
  6. AfricaRice Sahel Station, Saint-Louis, Senegal.

    • Isaac Kofi Bimpong
  7. AfricaRice Centre, Cotonou, Benin.

    • Marie-Noelle Ndjiondjop

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Contributions

R.S.M., G.B.G. and M.D.P. designed the experiments and analyses. I.K.B. and M.-N.N. helped in design and execution of the fieldwork in Senegal and Togo, respectively. R.S.M., M.S., A.P., J.A., A.B., K.D., B.G. and G.B.G. collected the data. R.S.M., J.Y.C., J.M.F., K.M.H. and M.D.P. analyzed the data. R.S.M., J.Y.C., D.Q.F. and M.D.P. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael D Purugganan.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8, Supplementary Tables 4 and 11, and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

    Sample data set.

  2. 2.

    Supplementary Table 2

    Sanger sequencing to genotype SNPs.

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    Supplementary Table 3

    Principal-component analysis of SNP variation.

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    Supplementary Table 5

    Salt tolerance phenotypes.

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    Supplementary Table 6

    Kruskal–Wallis results of phenotypes.

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    Supplementary Table 7

    Kruskal–Wallis pairwise comparisons of phenotypes between geographic populations.

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    Supplementary Table 8

    GWAS results.

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    Supplementary Table 9

    Significant 10-kb window coordinates and their maximum XPCLR values.

  9. 9.

    Supplementary Table 10

    Significant FST regions between NW coast and SW coast populations.

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DOI

https://doi.org/10.1038/ng.3633