A western Sahara centre of domestication inferred from pearl millet genomes

Abstract

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.

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Acknowledgements

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).

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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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The authors declare no competing interests.

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Supplementary data, models, references, tables and figures

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Supplementary Table 1

Passport data

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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