Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio (Digitaria exilis)

Fonio (Digitaria exilis), known as the "grain of life," is a vital food security crop grown by smallholder farmers across West Africa. Renowned for its short maturity period of 6-8 weeks, fonio provides essential harvests during periods of food scarcity. Its nutritional value, drought resilience, and ability to thrive on marginal soils make it a crucial staple in the region. However, fonio’s yield, averaging less than 0.5 metric tons per hectare, remains significantly lower than major cereals, due to minimal breeding efforts aimed at enhancing agronomic traits. In this study, we generated a high-quality chromosome-resolved, tetraploid (2n=4x=36) genome of a fonio line (PI 349688) available through the United States Germplasm Resource Information Network (GRIN). Time-of-day (TOD) expression profiling revealed sub-genome dominance in pathways associated with key agronomic traits that were also identified in a selective sweep analysis across a panel of 90 fonio accessions that originated from 21 different villages over five regions of Senegal representing eight distinct ethnic groups. Leveraging phenotyping across 14 key agronomic traits, we identified genotype-trait associations for plant height, tillering and panicle yield with genes involved in the circadian clock, light signaling and plant architecture. We demonstrated that fonio is amenable to transformation and gene editing, as evidenced by successful CRISPR-Cas9 modification of the Green Revolution gene REDUCED HEIGHT 1 (RHT1), resulting in lines with increased height, vegetative area, and enhanced tillering. Collectively, the genomic resources developed here pave new avenues for molecular breeding and trait discovery, laying a robust foundation for accelerating fonio improvement to bolster food security, climate resilience, and sustainable agriculture in West Africa.