GhAP1-D3 promote flowering by transcriptionally repressing the cold shock protein gene GhEFP1 in upland cotton

Flowering time is a key determinant of regional adaptation and early maturity in upland cotton. However, the genetic mechanisms governing flowering-time regulation during modern cotton breeding remain largely unknown. In this study, we integrated identity-by-descent (IBD) analysis, selective sweep mapping, and genome-wide association studies (GWAS) to identify GhEFP1 , which encodes a cold shock domain-containing protein, as a candidate regulator of flowering time in upland cotton from the Yangtze River cotton-growing region. Haplotype analysis confirmed that GhEFP1 underwent strong artificial selection during the breeding of early-maturing cultivars. Functional analyses demonstrated that silencing GhEFP1 accelerated the floral transition and promoted floral bud differentiation, whereas ectopic overexpression delayed flowering, indicating that GhEFP1 plays a negative regulatory role in cotton flowering. Mechanistically, flowering-related MADS-box transcription factor GhAP1-D3 directly bind to the GhEFP1 promoter and repressed its transcription. Consistent with this regulatory relationship, the biological functions of GhAP1-D3 were opposite to those of GhEFP1 . Together, our results uncover a novel role of cold shock proteins in the regulation of flowering and establish the GhAP1-D3– GhEFP1 regulatory module that controls floral transition in upland cotton. This work reveals novel aspects of the molecular basis governing flowering time and identifies natural allelic variants of GhEFP1 as candidate targets for modifying flowering time, an important component of early maturity.