Dexi Niatia 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.

半矮秆、抗倒伏的水稻与小麦品种是20世纪60至70年代绿色革命的关键支撑品种，至今仍在全球育种项目中被广泛应用。在小麦中，REDUCED HEIGHT 1（RHT1）——作为赤霉素（GA）信号通路关键抑制因子的DELLA蛋白家族成员——的突变可赋予植株半矮秆株型并提升倒伏抗性。受此策略启发，我们借助CRISPR-Cas9技术对福尼奥（Fonio）进行基因编辑，通过在RHT1直系同源基因的保守DELLA结构域（天冬氨酸-谷氨酸-亮氨酸-亮氨酸-丙氨酸）引入框内缺失，获得了半矮秆、抗倒伏的福尼奥材料。为验证编辑效果，我们对编辑所用的野生型（WT）福尼奥株系，以及编辑植株的T1、T2、T3代群体分别构建了染色体级、单倍型解析的基因组组装结果。所有基因组均采用PacBio Revio平台进行测序，通过HiFiasm完成组装，并以已发表的福尼奥参考基因组为参照，借助RagTag进行基因组脚手架构建。