Relief of GbDEAH12G repression on the GbNAC072C-GbHOX3 axis improves lint percentage in Gossypium barbadense

Improving lint percentage (LP) is a key breeding target for Sea Island cotton (Gossypium barbadense), yet its genetic basis remains poorly understood. Here, we identify GbNAC072C as a positive regulator of LP that promotes fiber cell protrusions by directly activating the transcription of GbHOX3. We find that GbNAC072C is inhibited by GbDEAH12G, and crucially, the strength of this interaction is haplotype-dependent. The GbDEAH12G protein binds GbNAC072C with higher affinity than the GbDEAH12C variant, leading to stronger suppression of GbHOX3 activation and consequently lower LP. This explains why the GbDEAH12C-GbNAC072C allele combination gives improved LP. Our work elucidates how haplotype-specific protein interactions modulate a key transcriptional cascade and proposes a disinhibition strategy for breaking yield limits in Sea Island cotton breeding. Lint percentage (LP) is a key component trait of cotton lint yield. Here, the authors identify GbNAC072C as a positive regulator of LP in Sea Island cotton (Gossypium barbadense) and characterize its interactions with GbDEAH12G, an ATP‑dependent RNA helicase, and GbHOX3, a homeodomain transcription factor.