Wheat domestication gene <i>Q</i> interplays with <i>TaARF12</i> to antagonistically modulate plant architecture by integrating multiple hormone homeostasis

Wheat domestication gene Q controls threshability and also pleiotropically affects plant morphogenesis. However, its specific roles in modulating plant architecture and the underlying mechanisms remain unclear. We dissected Q effects on plant architecture using transgenic overexpression and knockout assays. The analyses of micromorphological and dynamic imaging, physiological productivity, multi-omics, and molecular interaction were performed to dissect the underlying regulatory mechanism. Allelic variation and genetic effect assays were employed to identify desirable haplotypes. The domesticated Q allele 5AQ in wild-type lines optimized plant architecture and endowed yield gain by modulating cell size of stem internodes and flag leaves, tiller initiation and outgrowth, and photosynthetic capacity. Q regulated many homologs of previously reported functional genes controlling plant architecture, multiple hormone homeostasis, and cell wall components. Q upregulated plant architecture regulators TaARF12-2B and TaARF12-2D by binding to the promoters. However, Q and the TaARF12 genes antagonistically modulate plant architecture. The favorable haplotypes of TaARF12-2B and the functional variation site were identified, and their origin, spread, and distribution were also traced. These findings specify the Q function in controlling plant architecture and yield formation, broaden insights into the underlying mechanism, and provide new molecular tools for wheat improvement.