Abstract

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 controlling fruit branch angle (FBA), remains largely unknown. This study identified qFBA-A11, a major QTL regulating FBA, using a Gossypium hirsutum × G. mustelinum introgression lines population. Map-based cloning revealed that GhFBA1_At was the major gene positively regulating FBA. GhFBA1_At encodes a protein with no known functional domains. Further investigations identified that GATA5, a light-responsive transcription factor, is a positive regulator of GhFBA1_At expression. The GhFBA1_At protein inhibited KNAT7 accumulation through direct protein-protein interaction and downregulated the expression of cell wall biosynthesis-related genes. This process promoted 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 caused complete gene loss, resulting in a compact plant architecture. Phylogenetic analysis showed that this SV was unique to G. mustelinum. CRISPR-Cas9 editing of GhFBA1_At generated a compact plant architecture and enhanced cotton yield under high-density planting. Our findings established GhFBA1_At as a crucial regulator of FBA, elucidated its molecular mechanism, and provided valuable germplasm resources for ideal plant architecture breeding in cotton.