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Domestication history and geographical adaptation inferred from a SNP map of African rice

Nature Genetics volume 48, pages 1083–1088 (2016)Cite this article

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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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Figure 1: A SNP map for African rice.
Figure 2: Population structuring in African rice.
Figure 3: Demography of O. glaberrima and O. barthii.
Figure 4: Population phenotypic differentiation, GWAS mapping and selective sweep analysis for salinity tolerance.
Figure 5: Comparison of GWAS and selected genomic regions at the proximal end of chromosome 4.

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Sequence Read Archive

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Sequence Read Archive

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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

Authors and 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. Genetics and Biotechnology Division, Plant Breeding, 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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  1. Rachel S Meyer
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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.

Corresponding author

Correspondence to Michael D Purugganan.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Tables 4 and 11, and Supplementary Note (PDF 530 kb)

Supplementary Table 1

Sample data set. (XLSX 500 kb)

Supplementary Table 2

Sanger sequencing to genotype SNPs. (XLSX 494 kb)

Supplementary Table 3

Principal-component analysis of SNP variation. (XLSX 496 kb)

Supplementary Table 5

Salt tolerance phenotypes. (XLSX 35 kb)

Supplementary Table 6

Kruskal–Wallis results of phenotypes. (XLSX 75 kb)

Supplementary Table 7

Kruskal–Wallis pairwise comparisons of phenotypes between geographic populations. (XLSX 72 kb)

Supplementary Table 8

GWAS results. (XLSX 43 kb)

Supplementary Table 9

Significant 10-kb window coordinates and their maximum XPCLR values. (XLSX 40 kb)

Supplementary Table 10

Significant FST regions between NW coast and SW coast populations. (XLSX 488 kb)

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Meyer, R., Choi, J., Sanches, M. et al. Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat Genet 48, 1083–1088 (2016). https://doi.org/10.1038/ng.3633

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