Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF ‐ PRUNING orthologs

Summary Domestication of upland cotton ( Gossypium hirsutum ) converted it from a lanky photoperiodic perennial to a day‐neutral annual row‐crop. Residual perennial traits, however, complicate irrigation and crop management, and more determinate architectures are desired. Cotton simultaneously maintains robust monopodial indeterminate shoots and sympodial determinate shoots. We questioned if and how the FLOWERING LOCUS T/ SINGLE FLOWER TRUSS ( SFT )‐like and TERMINAL FLOWER 1/ SELF ‐ PRUNING ( SP )‐like genes control the balance of monopodial and sympodial growth in a woody perennial with complex growth habit. Virus‐based manipulation of Gh SP and Gh SFT expression enabled unprecedented functional analysis of cotton development. Gh SP maintains growth in all apices; in its absence, both monopodial and sympodial branch systems terminate precociously. Gh SFT encodes a florigenic signal stimulating rapid onset of sympodial branching and flowering in side shoots of wild photoperiodic and modern day‐neutral accessions. High florigen concentrations did not alter monopodial apices, implying that once a cotton apex is SP ‐determined, it cannot be reset by florigen. Gh SP is also essential to establish and maintain cambial activity. Dynamic changes in Gh SFT and Gh SP levels navigate meristems between monopodial and sympodial programs in a single plant. SFT and SP influenced cotton domestication and are ideal targets for further agricultural optimization.