Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

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
established 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.