Dibu WT Transformation 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（Green Revolution）的关键种质，至今仍在全球育种项目中被广泛推广应用。在小麦中，作为赤霉素（GA）信号通路关键阻遏因子的DELLA蛋白家族成员REDUCED HEIGHT 1（RHT1）发生突变后，可赋予植株半矮秆表型并提升抗倒伏能力。受此育种策略启发，本研究利用CRISPR–Cas9技术，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）中引入框内缺失，成功创制了半矮秆、抗倒伏的福尼奥粟（Fonio）。为验证编辑效果，我们对编辑实验所用的野生型（WT）福尼奥粟株系，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序列。所有基因组均通过PacBio Revio测序平台完成测序，采用HiFiasm软件进行组装，并以已公开的福尼奥粟参考基因组为参考，通过RagTag工具完成基因组脚手架挂载。