Genome-Wide Characterization of the GT4 Gene Family in Cotton

The glycosyltransferase 4 (GT4) family plays essential roles in plant cell wall biosynthesis, glycolipid metabolism, and secondary metabolite glycosylation, yet its characterization in cotton remains scarce. Here, we performed a genome-wide identification of GT4 genes in four cotton species using comprehensive bioinformatics approaches, and systematically analyzed their conserved motifs, gene structures, chromosomal distributions, phylogeny, and selection pressures. A total of 49 GT4 members were identified, including seven genes in G. arboreum (A2), nine genes in G. raimondii (D5), 16 genes in G. hirsutum (AD1), and 17 genes in G. barbadense (AD2). Phylogenetic analysis classified them into four subfamilies. Chromosomal mapping revealed uneven distribution and various duplication events. Promoter cis-element analysis indicated enrichment of light-, phytohormon-, and stress-responsive regulatory elements. Selection pressure analysis indicated predominant purifying selection among homologous pairs. Expression profiling across multiple tissues, fiber developmental stages, and four abiotic stresses (cold, drought, salt, and heat) identified GhGT4_10 and GhGT4_2 as stress-responsive candidate genes; GhGT4_10 showed the most pronounced induction across the tested stresses, and both were drought-responsive by qRT-PCR. WGCNA under drought stress showed that the MEgreen module was most positively correlated with the 12 h post-treatment time point, and this module was significantly enriched in genes annotated to chloroplast components, photoresponse pathways, ribosomal machinery, and glyoxylate/dicarboxylate metabolism. Subcellular localization showed that GhGT4_2 localizes to chloroplasts, consistent with its predicted localization; this observation supports a possible chloroplast-associated role but does not establish its function or involvement in a specific pathway. In fuzz development analysis, the MEturquoise module was highly correlated with fuzz phenotype, and a co-expression network centered on GhGT4_15 identified 503 network-connected genes enriched in nucleocytoplasmic transport, phagosome, and spliceosome pathways. These enrichment results suggest a hypothesis that GhGT4_15 may be associated with these pathways. qRT-PCR showed that GhGT4_2 and GhGT4_10 were drought-responsive, whereas GhGT4_7 and GhGT4_15 were associated with fuzz development and represent candidate regulators, including possible negative regulation, pending functional validation. Collectively, this study characterizes the structural and expression features of the cotton GT4 family and provides candidate genes for molecular breeding targeting abiotic stress resistance and fiber trait improvement; functional validation is needed to establish causal roles.