Independent domestication and cultivation histories of two West African indigenous fonio millet crops

Thomas Kaczmarek (), Philippe Cubry, Louis Champion, Sandrine Causse, Marie Couderc, Julie Orjuela, Edak A. Uyoh, Happiness O. Oselebe, Stephen N. Dachi, Charlotte O. A. Adje, Emmanuel Sekloka, Enoch G. Achigan-Dako, Abdou R. Ibrahim Bio Yerima, Sani Idi Saidou, Yacoubou Bakasso, Baye M. Diop, Mame C. Gueye, Richard Y. Agyare, Joseph Adjebeng-Danquah, Mathieu Gueye, Jan J. Wieringa, Yves Vigouroux (), Claire Billot (), Adeline Barnaud () and Christian Leclerc ()
Additional contact information
Thomas Kaczmarek: UMR AGAP Institut
Philippe Cubry: DIADE, University of Montpellier, IRD, CIRAD
Louis Champion: DIADE, University of Montpellier, IRD, CIRAD
Sandrine Causse: UMR AGAP Institut
Marie Couderc: DIADE, University of Montpellier, IRD, CIRAD
Julie Orjuela: DIADE, University of Montpellier, IRD, CIRAD
Edak A. Uyoh: University of Calabar
Happiness O. Oselebe: Ebonyi State University
Stephen N. Dachi: University of Jos
Charlotte O. A. Adje: University of Abomey-Calavi
Emmanuel Sekloka: LaPAPP, University of Parakou
Enoch G. Achigan-Dako: University of Abomey-Calavi
Abdou R. Ibrahim Bio Yerima: University of Abomey-Calavi
Sani Idi Saidou: University of Diffa
Yacoubou Bakasso: Abdou Moumouni Univyersit
Baye M. Diop: Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS)
Mame C. Gueye: Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS)
Richard Y. Agyare: Council for Scientific and Industrial Research—Savanna Agricultural Research Institute (CSIR-SARI)
Joseph Adjebeng-Danquah: Council for Scientific and Industrial Research—Savanna Agricultural Research Institute (CSIR-SARI)
Mathieu Gueye: Université Cheikh Anta Diop
Jan J. Wieringa: Naturalis Biodiversity Center
Yves Vigouroux: DIADE, University of Montpellier, IRD, CIRAD
Claire Billot: UMR AGAP Institut
Adeline Barnaud: DIADE, University of Montpellier, IRD, CIRAD
Christian Leclerc: UMR AGAP Institut

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Crop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. Black and white fonio (Digitaria iburua and D. exilis, respectively) are two small indigenous grain cereals grown in West Africa. The relationship between these two cultivated crops and wild Digitaria species is still unclear. Here, we analyse whole genome sequences of 265 accessions comprising these two cultivated species and their close wild relatives. We show that white and black fonio were the result of two independent domestications without gene flow. We infer a cultivation expansion that began at the outset of the CE era, coinciding with the earliest discovered archaeological fonio remains in Nigeria. Fonio population sizes declined a few centuries ago, probably due to a combination of several factors, including major social and agricultural changes, intensification of the slave trade and the introduction of new, less labour-intensive crops. The key knowledge and genomic resources outlined here will help to promote and conserve these neglected climate-resilient crops and thereby provide an opportunity to tailor agriculture to the changing world.

Date: 2025
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DOI: 10.1038/s41467-025-59454-2

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