Dexi KAUST Assembly Files

Semidwarf, lodging-tolerant rice and wheat varieties were pivotal to the Green Revolution of the 1960s and 1970s and continue to be widely adopted in global breeding programs. In wheat, mutations in REDUCED HEIGHT 1(RHT1), a member of the DELLA protein family that functions as a key repressor in the gibberellin (GA) signaling pathway, confer semidwarf stature and improved lodging resistance. Inspired by this strategy, we used CRISPR–Cas9 to engineer semidwarf, lodging-tolerant Fonio by introducing an in-frame deletion within the conserved DELLA domain (Aspartate–Glutamate–Leucine–Leucine–Alanine) of the RHT1 ortholog. We validated the edits by generating chromosome-scale, haplotype-resolved genome assemblies for the wild-type (WT) Fonio line used in editing, as well as for the T1, T2, and T3 generations of edited plants. All genomes were sequenced using PacBio Revio, assembled with HiFiasm, and scaffolded with RagTag using the existing Fonio reference genome as a guide.