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

Summary 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.