The domesticated SiSD1 coordinates plant architecture and nitrogen metabolism to boost yield in foxtail millet

Foxtail millet has lagged in yield due to suboptimal architecture. Here we report a telomere-to-telomere genome assembly of the dwarf, more-tillering cultivar Dungu and identify SiSD1, which encodes GA20ox2, through map-based cloning. A loss-of-function sisd1 allele reduces bioactive gibberellins, conferring semi-dwarfism, increased tillering and panicle number, and higher yield across densities. Unlike rice SD1, sisd1 enhances ammonium uptake yet limits ammonium assimilation and nitrate uptake, reshaping nitrogen metabolism. Critically, the semi-dominantly heterozygous SiSD1/sisd1 in F1 hybrids optimally balances stature, tillering, and nitrogen acquisition to drive yield heterosis.Field trials and genotype surveys confirm the prevalence of this allele in elite commercial hybrids, including the Zhangzagu series. Surprisingly, D157E substitution in SiSD1 relative to its wild progenitor attenuates GA biosynthesis and was favored during domestication. Collectively, SiSD1 functions as a pleiotropic integrator of development and nutrient physiology, and the strategic deployment of its heterozygosity offers a targeted breeding paradigm for crop improvement.