Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

AGAP Université de Montpellier Cirad INRAE Institut Agro Montpellier France

Center for Desert Agriculture Biological and Environmental Science and Engineering Division Thuwal Saudi Arabia

CIRAD UMR AGAP Montpellier France

CNRGV Plant Genomics Center INRAE Toulouse France

Department of Plant and Microbial Biology University of Zurich Zürich Switzerland

DIADE Univ Montpellier IRD Montpellier France

Inari Agriculture One Kendall Square Building 600 700 Cambridge MA 02139 USA

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Hana for Biotechnological and Agricultural Research Olomouc Czech Republic

Laboratoire de Botanique Département de Botanique et Géologie IFAN Ch A Diop UCAD Dakar Senegal

Laboratoire Mixte International LAPSE Dakar Senegal

Naturalis Biodiversity Center Leiden the Netherlands

Senegalese Agricultural Research Institute Dakar Senegal

Supercomputing Core Lab King Abdullah University of Science and Technology Thuwal Saudi Arabia

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