Fonio (Digitaria exilis) Genome

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.