A western Sahara centre of domestication inferred from pearl millet genomes


There have been intense debates over the geographic origin of African crops and agriculture. Here, we used whole-genome sequencing data to infer the domestication origin of pearl millet (Cenchrus americanus). Our results supported an origin in western Sahara, and we dated the onset of cultivated pearl millet expansion in Africa to 4,900 years ago. We provided evidence that wild-to-crop gene flow increased cultivated genetic diversity leading to diversity hotspots in western and eastern Sahel and adaptive introgression of 15 genomic regions. Our study reconciled genetic and archaeological data for one of the oldest African crops.

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Fig. 1: Genetic diversity and origin of pearl millet domestication.
Fig. 2: Selection and introgression in pearl millet.


  1. 1.

    Vavilov, N. I. & Dorofeev, V. F. Origin and Geography of Cultivated Plants (Cambridge Univ. Press, Cambridge, 1992).

  2. 2.

    Harlan, J. R., De Wet, J. M. J. & Stemler, A. B. L. Origins of African Plant Domestication (De Gruyter, Berlin, 1976).

  3. 3.

    Harlan, J. R. Science 174, 468–474 (1971).

    CAS  Article  Google Scholar 

  4. 4.

    Varshney, R. K. et al. Nat. Biotechnol. 35, 969–976 (2017).

    CAS  Article  Google Scholar 

  5. 5.

    Hu, Z. et al. BMC Genom. 16, 1048 (2015).

    Article  Google Scholar 

  6. 6.

    Dussert, Y., Snirc, A. & Robert, T. Mol. Ecol. 24, 1387–1402 (2015).

    CAS  Article  Google Scholar 

  7. 7.

    Manning, K. in West African Archaeology: New Developments, New Perspectives (ed. Allsworth-Jones, P.) 43–52 (Archaeopress, Oxford, 2010).

  8. 8.

    Manning, K., Pelling, R., Higham, T., Schwenniger, J.-L. & Fuller, D. Q. J. Archaeol. Sci. 38, 312–322 (2011).

  9. 9.

    Ozainne, S. et al. J. Archaeol. Sci. 50, 359–368 (2014).

    Article  Google Scholar 

  10. 10.

    Oumar, I., Mariac, C., Pham, J.-L. & Vigouroux, Y. Theor. Appl. Genet. 117, 489–497 (2008).

    CAS  Article  Google Scholar 

  11. 11.

    Berthouly-Salazar, C. et al. Front. Plant Sci. 7, 777 (2016).

  12. 12.

    Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C. & Foll, M. PLoS Genet. 9, e1003905 (2013).

    Article  Google Scholar 

  13. 13.

    Cubry, P., Vigouroux, Y. & François, O. Front. Genet. 8, 139 (2017).

  14. 14.

    Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Nature 461, 489–494 (2009).

    CAS  Article  Google Scholar 

  15. 15.

    Pickrell, J. K. & Pritchard, J. K. PLOS Genet. 8, e1002967 (2012).

    CAS  Article  Google Scholar 

  16. 16.

    Kröpelin, S. et al. Science 320, 765–768 (2008).

    Article  Google Scholar 

  17. 17.

    Huerta-Sánchez, E. et al. Nature 512, 194–197 (2014).

    Article  Google Scholar 

  18. 18.

    Ai, H. et al. Nat. Genet. 47, 217–225 (2015).

    CAS  Article  Google Scholar 

  19. 19.

    Arnold, B. J. et al. Proc. Natl Acad. Sci. USA 113, 8320–8325 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Hufford, M. B. et al. PLoS Genet. 9, e1003477 (2013).

    CAS  Article  Google Scholar 

  21. 21.

    Nielsen, R. et al. Genome Res. 15, 1566–1575 (2005).

    CAS  Article  Google Scholar 

  22. 22.

    Dupuy, C. Encycl. Berbère XXXIX, 6529–6544 (2015).

    Google Scholar 

  23. 23.

    Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G. & François, O. Genetics 196, 973–983 (2014).

    Article  Google Scholar 

  24. 24.

    Frichot, E. & François, O. Methods Ecol. Evol. 6, 925–929 (2015).

    Article  Google Scholar 

  25. 25.

    R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2016).

  26. 26.

    Caye, K., Deist, T. M., Martins, H., Michel, O. & François, O. Mol. Ecol. Resour. 16, 540–548 (2016).

    CAS  Article  Google Scholar 

  27. 27.

    Excoffier, L. & Foll, M. Bioinformatics 27, 1332–1334 (2011).

  28. 28.

    Ray, N., Currat, M., Foll, M. & Excoffier, L. Bioinformatics 26, 2993–2994 (2010).

    CAS  Article  Google Scholar 

  29. 29.

    Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Trends Ecol. Evol. 25, 410–418 (2010).

    Article  Google Scholar 

  30. 30.

    Csilléry, K., François, O. & Blum, M. G. B. Methods Ecol. Evol. 3, 475–479 (2012).

    Article  Google Scholar 

  31. 31.

    Nielsen, R. et al. PLoS Biol. 3, e170 (2005).

    Article  Google Scholar 

  32. 32.

    Pavlidis, P., Živković, D., Stamatakis, A. & Alachiotis, N. Mol. Biol. Evol. 30, 2224–2234 (2013).

    CAS  Article  Google Scholar 

  33. 33.

    Weir, B. S. Genetic Data Analysis II: Methods for Discrete Population Genetic Data (Oxford Univ. Press, Oxford, 1996).

  34. 34.

    Weir, B. S. & Cockerham, C. C. Evolution 38, 1358–1370 (1984).

    CAS  Google Scholar 

  35. 35.

    Nei, M. & Li, W. H. Proc. Natl Acad. Sci. USA 76, 5269–5273 (1979).

    CAS  Article  Google Scholar 

  36. 36.

    Cruickshank, T. E. & Hahn, M. W. Mol. Ecol. 23, 3133–3157 (2014).

    Article  Google Scholar 

  37. 37.

    Bass, J. D., Dabney, A. & Robinson, D. qvalue: Q-value Estimation for False Discovery Rate Control R package version 2.12.0 (2015).

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We are grateful to the Genotoul sequencing platform Toulouse Midi-Pyrenees for help during sequencing. We also want to thank N. Tando and the IRD itrop Plantes Santé bioinformatic platform for providing HPC resources and support for our research project. Y.V. acknowledges support from the Agence Nationale de la Recherche (ANR-13-BSV7-0017). C.B.-S. acknowledges support from Agropolis Fondation under the reference ID 1403-057 through the Investissements d’avenir programme (Labex Agro: ANR-10-LABX-0001-01).

Author information




C.B., P.C., N.A.K., A.B., O.F., C.B.-S. and Y.V. designed the analysis. C.B. and P.C. performed statistical analyses. C.M. and M.C. performed additional experimental work. B.R., N.S., C.D., M.T., C.S. and O.F. contributed to analytic tools, data, methods and participated in data analysis; X.L., X.X., R.K.V. and Y.V. managed and designed the pearl millet genome project. O.F., C.B.-S. and Y.V. managed this genomic diversity study. C.B., P.C., C.B.-S. and Y.V. wrote the manuscript.

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Correspondence to Concetta Burgarella or Philippe Cubry or Olivier François or Cécile Berthouly-Salazar or Yves Vigouroux.

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Supplementary Table 7

Gene models and annotation for genomic regions under selection

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Burgarella, C., Cubry, P., Kane, N.A. et al. A western Sahara centre of domestication inferred from pearl millet genomes. Nat Ecol Evol 2, 1377–1380 (2018). https://doi.org/10.1038/s41559-018-0643-y

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