The GATA5–GhFBA1_At–KNAT7 module regulates fruit branch angle and high-density yield by controlling cell expansion and cell wall thickness in cotton

Enhancing cotton yield remains a paramount breeding objective. Given limited arable land, increasing planting density is an effective strategy to boost cotton yield. However, the genetic basis of plant architecture suitable for high-density planting, particularly the molecular mechanism that controls fruit branch angle (FBA), remains largely unknown. Here, we identified qFBA-A11, a major quantitative trait locus associated with FBA, using a Gossypium hirsutum × Gossypium mustelinum introgression line population. Map-based cloning revealed that GhFBA1_At, whose encoded protein has no known functional domains, is the major gene positively regulating FBA. Further investigations demonstrated that GATA5, a light-responsive transcription factor, positively regulates GhFBA1_At expression. GhFBA1_At protein inhibits KNAT7 accumulation through a direct protein-protein interaction and downregulates the expression of genes related to cell wall biosynthesis. This process promotes cell expansion while reducing cell wall thickness, ultimately weakening the mechanical strength of the cell wall and leading to a loose plant architecture. A structural variation (SV) at the GhFBA1_At locus in G. mustelinum causes complete gene loss, resulting in a compact plant architecture. Phylogenetic analysis showed that this SV is unique to G. mustelinum. CRISPR-Cas9 editing of GhFBA1_At produced a compact plant architecture and enhanced cotton yield under high-density planting. Our findings establish GhFBA1_At as a crucial regulator of FBA, reveal its molecular mechanism, and provide valuable germplasm resources for ideal plant architecture breeding in cotton.