Genome-Wide Characterization of the LRX Gene Family in Three Cotton Species and Preliminary Evidence Linking GhLRX2/GhLRX19 to Plant Height in Upland Cotton

Plant height is an important agronomic trait affecting cotton architecture and mechanized production. Leucine-rich repeat extensins (LRXs) are cell-wall-associated proteins involved in cell-wall organization, cell elongation, and cell-wall integrity signaling. In this study, genome-wide analysis of Gossypium hirsutum, G. arboreum, and G. raimondii identified 74 LRX loci, comprising 36 GhLRX, 19 GaLRX, and 19 GrLRX genes. These 74 loci were represented by 79 annotated protein models, including five additional models from three GrLRX loci. Maximum-likelihood phylogenetic analysis of 74 representative cotton proteins and 11 Arabidopsis proteins assigned them to four descriptive groups. Of the 79 protein models, 75 were predicted to contain Sec/SPI-type signal peptides. Conserved motif and gene structure analyses revealed broadly similar organization with variation among members and alternative isoforms. Promoter analysis identified putative hormone- and stress-related cis-acting elements. Collinearity analyses revealed syntenic relationships within upland cotton and with its diploid relatives. Public transcriptome data showed variation in GhLRX transcript abundance across tissues, developmental stages, and abiotic stress conditions. The homoeologous genes GhLRX2 and GhLRX19 showed relatively high transcript abundance in stems and 20-day-post-anthesis fibers and were selected for preliminary investigation. Virus-induced gene silencing (VIGS) treatment targeting a sequence shared by GhLRX2 and GhLRX19 was associated with lower combined transcript abundance and reduced plant height. These findings provide preliminary evidence linking this shared-sequence VIGS treatment to reduced plant height, while the individual responses and functions of the two homoeologs remain unresolved.