Transcriptional Regulation of SWEET15_A01 by MYB44 / bHLH3 Modulates Carbon Allocation in Cotton Ovule and Fibre to Affect Seed and Fibre Traits

ABSTRACT The allocation of carbon sources between cotton ovule and fibre significantly influences the yield and quality of seed and fibre. SWEET15 (Sugars Will Eventually be Exported Transporter 15) plays a key role in sucrose transport; however, the transcriptional regulation of SWEET15 in cotton remains unclear. Here, a SWEET15_A01 , predominantly expressed during late ovule development (25–35 DPA), functions as a sucrose transporter between the ovule and fibre in cotton. Promoter variations between sea‐island and upland cottons correlate with differential expression and cottonseed oil content. Overexpressing SWEET15_A01 in upland cotton reduces fibre length, seed size and oil content but increases lint percentage. Downregulation of SWEET15_A01 in upland cotton ovules upregulates other sugar transporters and cellulose synthase genes ( CesA s) in fibres, indicating compensatory mechanisms. The R2R3‐MYB transcription factor MYB44 directly binds to the SWEET15_A01 promoter, suppressing its expression, while bHLH3 interacts with MYB44 to weaken this repression. Overexpressing MYB44 increases fibre length but reduces seed size and oil content. This study reveals genetic variations for cottonseed oil improvement and elucidates how the MYB44/bHLH3‐SWEET15_A01 module coordinates sugar allocation to balance seed and fibre development, offering strategies for enhancing cottonseed oil content.