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.

Long non-coding RNAs (lncRNAs) have emerged as important regulatory molecules in plants, but their potential roles during modern maize breeding remain largely unexplored. This study systematically characterized lncRNA expression dynamics using transcriptome data from 137 maize inbred lines from different breeding eras in China. We identified 18,023 lncRNAs transcripts, grouped by expression trends across historical breeding eras. Comparative analysis revealed 2228 differentially expressed lncRNAs transcripts (DElncRNAs) between modern (CN2000&10s) and early (CN1960&70s) accessions. By integrating WGCNA and cis-target analysis, we identified candidate lncRNAs and putative lncRNA-PCG associations that may be associated with maize plant architecture-related processes. Further, 771 DElncRNAs were predicted to be associated with 810 protein-coding genes, and these associated genes were significantly enriched in plant hormone signal transduction. Dual-luciferase reporter assays provided preliminary experimental support that lncrna.33063 and lncrna.33068 can repress the promoter activity of ZmPIF5.2 in a heterologous transient expression system. Furthermore, we constructed a putative ceRNA-related candidate interaction network consisting of lncRNA–miRNA–mRNA triplets that include 317 candidate miRNA-lncRNA pairs and 8325 candidate miRNA-mRNA pairs, with the associated mRNAs enriched in biological processes such as morphogenesis, stimulus response, and hormone metabolism. These findings provide a set of candidate lncRNAs and lncRNA-PCG associations for future functional validation and may offer useful clues for understanding the possible roles of lncRNAs in agronomic trait-related biological processes and maize molecular breeding. Overall, this study provides candidate genetic resources and a framework for future investigation of lncRNA-associated relationships potentially related to agronomic trait variation in maize.