Fonio Assembly Files

Fonio is an ancient food security crop grown by smallholder farmers in West Africa, valued as the 'grain of life' for its short maturity period of 6-8 weeks, allowing for harvests during periods of food scarcity. Its nutritional value, drought tolerance, and ability to grow on marginal land make it a crucial staple in the region. Despite this, yields of fonio remain significantly lower than major cereals, at less than 0.5 metric tons per hectare, due to minimal focus on improving agronomic traits. Here, we present a chromosome-resolved tetraploid (2n=4x=36) genome of fonio, which retains a core grass gene order with minimal genome fractionation. Our analysis shows that this tetraploidy likely represents an allotetraploid event between closely related species, with time-of-day (TOD) expression sampling revealing sub-genome dominance in key agronomic pathways. Phenotypic analysis of a Senegalese breeding population identifies light signaling genes as key factors in controlling tillering and biomass. We also find a significant signature of selection at the 'weeping gene' LAZY1, which is associated with increased yield due to its influence on plant architecture. Finally, we demonstrate that the sequenced fonio genome is amenable to transformation, providing a path forward for improving this crop through modern molecular breeding techniques.