Background: The GhA01EP1 gene in upland cotton encodes an epidermal-specific secreted glycoprotein, whose functional characterization remains unexplored beyond our initial discovery of its water deficit resistance association. Therefore, we further designed experiments to investigate the functional role of GhA01EP1. Methods: We sequenced and analyzed the transcriptomes of wild-type (Col-0) and GhA01EP1-transgenic Arabidopsis thaliana. The differences in morphological and biochemical indicators were examined. In addition, the proteins interacting with GhA01EP1 in Arabidopsis were screened using a glutathione-S-transferase pull-down assay. Results: The GhA01EP1-transgenic Arabidopsis plants flowered earlier, produced more branches, and had a higher seed yield than Col-0. Transcriptome analysis revealed that differentially expressed genes detected in the comparison of GhA01EP1-transgenic and Col-0 Arabidopsis under the water treatment (the control) were associated especially with circadian rhythm regulation, photoperiodic flowering reaction, hormone metabolism, glyoxalase I synthesis, antioxidant pathway, branching development, and carbon-nitrogen allocation. Under water-sufficient or water-deficient treatments, the glyoxalase I activity and lignin content of GhA01EP1-transgenic Arabidopsis were significantly higher. Under water deficit stress, the malondialdehyde and starch contents were significantly lower, while peroxidase activity and protein content were significantly higher than those of Col-0. Conclusions: GhA01EP1 synergistically improved the precocity, water deficit tolerance, and seed yield of GhA01EP1-transgenic Arabidopsis. Analysis of GhA01EP1 function provides a molecular basis for breeding improved cotton varieties.

Plant SABATH methyltransferases contribute to volatile formation, hormone homeostasis and stress responses, but their family-wide organization in sunflower remains poorly characterized. Using the HanXRQr2.0-SUNRISE reference genome, we identified 33 high-confidence HaSABATH genes and integrated phylogenetic, duplication, synteny, promoter and protein-structure analyses with expression profiles from 200 public RNA sequencing (RNA-seq) libraries representing 87 distinct conditions. Twelve genes belonged to the salicylic acid/jasmonic acid methyltransferase-related Clade I, 19 to the benzoic acid/salicylic acid methyltransferase-related Clade II, and two to other lineages. Tandem, proximal, dispersed and whole-genome/segmental duplication contributed to the family, with overlapping tandem and segmental evidence for HaSABATH4 and HaSABATH15. Eleven reliable nonsynonymous-to-synonymous substitution ratios were below one. Most predicted proteins showed high model confidence. Across the sampled conditions, Clade I members generally showed higher expression levels and broader expression, while many Clade II members were weakly expressed or condition-biased. HaSABATH4 and HaSABATH6 were prioritized for follow-up under combined saline–alkali stress. This integrated analysis links evolutionary context to expression divergence and provides candidates for targeted biochemical and genetic studies.

In this study, we performed the first genome-wide identification and characterization of the cinnamoyl-CoA reductase (CCR) gene family in upland cotton (Gossypium hirsutum), focusing on its potential association with stem strength. We identified 76 GhCCR genes and classified them into four subfamilies. We then analyzed their evolutionary relationships, conserved domains, synteny, promoter cis-elements, and expression patterns. All GhCCR proteins possess the NADB_Rossmann superfamily domain, and family expansion appears to have been driven mainly by segmental and tandem duplications. A small number of GhCCR genes showed relatively high expression in leaf, pistil, and torus tissues, while genes such as GhCCR3/9/10 exhibited elevated transcript levels under abiotic stress conditions. RT-qPCR results indicated that three candidate GhCCR genes (GhCCR25, GhCCR52 and GhCCR64) were significantly more highly expressed in multiple tissues of the stiff-stem line JY-25 than in the soft-stem line JR-15. Together, these findings suggest that GhCCR genes may contribute to the regulation of growth, development, and stress adaptation in G. hirsutum. However, direct biochemical or genetic validation is required to confirm their functional roles in lignin biosynthesis and stem rigidity.