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Studying plant domestication helps us to understand not only the origins of agriculture, but also how relationships between domesticated species, their wild relatives, human societies and environments have shaped cultivated diversity. Crop diversification is widely recognized as a cornerstone of resilient agriculture and sustainable food systems. However, genomic studies of crop evolutionary history have mostly focused on major staples such as rice, maize and wheat. As a result, research into the domestication of traditional species, mainly grown in smallholder farming systems, has long been overlooked. This is particularly true for sub-Saharan crops such as black fonio (Digitaria iburua) and white fonio (Digitaria exilis), which are recognized for their agronomic and nutritional properties.

The goal of this study was to determine when and how these two species were domesticated, in particular whether or not their domestication processes were independent, and to reveal the dynamics linked to these processes. To do so, the scientists assembled a vast collection of genomic resources comprising 265 accessions of the two cultivated species and their wild relatives. Among these accessions, the first complete genome sequences of black fonio (Digitaria iburua) and its wild relative (Digitaria ternata) were obtained. In addition, new full genome sequences of white fonio (Digitaria exilis) were generated in order to provide a representative and near-complete picture of its geographical distribution.

In this study, the researchers showed that black fonio and white fonio form two distinct gene pools. They used a combination of complementary genomic approaches and methods, providing robust evidence for two independent domestication events with no gene flow, despite the crops having similar appearances and uses, and sometimes being grown in the same areas. Demographic modelling suggests that the expansion of fonio cultivation began at the outset of the CE era, coinciding with the earliest discovered archaeological fonio remains in Nigeria. Fonio cultivation then appears to have declined from the 16th century onwards, probably due to major sociodemographic changes linked to European colonization, such as the introduction of new crops like maize and rice, as well as the intensification of the slave trade.

The insights gained from this study are crucial to understanding the spatial and temporal dynamics of crop domestication in sub-Saharan Africa. The findings are also key to better conserving diversity in the face of climate change, and to promoting the wider use of these species, while ensuring that any financial, nutritional or other benefits derived from their use are shared with local communities.

Reference

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*, Christian Leclerc*. , Nature Communications, 16, 4067 (2025).    

* These authors contributed equally.

This publication is the result of PhD and postdoctoral research by Thomas Kaczmarek, conducted in collaboration with AGAP Institut and the Diversity, Adaptation, Development of Plants (DIADE) Joint Research Unit (UMR).

French funding for this research: European Union Horizon 2020 EWA-BELT (862848, ‘Linking East and West African farming systems experience into a BELT of sustainable intensification’) and ANR AfriCrop project (ANR-13-BSV7-0017).