Identification and functional characterization of GhCSLD3, a negative regulator of fruit branch elongation in cotton (Gossypium hirsutum L.).

The fruit branch is a critical determinant of plant architecture in cotton, and its length optimization is pivotal for high-density planting and mechanical harvesting. However, the genetic mechanisms governing fruit branch length (FBL) are not fully elucidated. In this study, an F2 population was generated from two contrasting upland cotton cultivars, Blanco3363 (BL, compact) and Sanjiang (SJ, loose). Using two different methodologies of bulked-segregant analysis (BSA)-seq, we identified three stable overlapping QTLs on chromosomes A08 (119.8-122.46 Mb), D01 (7.51-10.10 Mb), and D09 (16.33-18.00 Mb). Integrative transcriptomic profiling and gene silencing selected a strong candidate gene, Cellulose synthase-like D3 (GhCSLD3), which is proposed to participate in hemicellulose polysaccharide biosynthesis or deposition on chromosome A08. GhCSLD3 exhibited higher expression in the apical meristem and fruit branch internodes of the short-branched BL compared to SJ. Silencing GhCSLD3 in cotton significantly increased fruit branch length, whereas overexpression in Arabidopsis thaliana resulted in shorter lateral branches. These findings suggest that GhCSLD3 may act as a negative regulator of fruit branch internode elongation, revealing an unconventional negative regulatory role of the CSLD family in defining plant branching architecture. Our findings provide a valuable target gene for molecular breeding to develop compact cotton cultivars suitable for modern mechanized production systems.