MLO (Mildew Resistance Locus O) genes encode seven-transmembrane proteins that function as critical regulators of powdery mildew resistance and abiotic stress responses. Despite their established importance, the MLO gene family in Gossypium hirsutum L. has not been systematically investigated under salt stress conditions. Here, we performed genome-wide identification of 46 GhMLO members using Hidden Markov Model and BLAST searches based on the latest cotton genome assembly. Phylogenetic analysis classified these genes into four distinct subfamilies. Transmembrane topology and conserved domain analyses revealed that all GhMLO proteins contain typical MLO domains and transmembrane structures, maintaining high structural similarity with dicotyledonous model plants. Synteny analysis demonstrated that the expansion of the GhMLO family was primarily driven by segmental and tandem duplications. Integration of transcriptomic data from the COTTONOMICS database revealed tissue-specific expression patterns, with higher transcript abundance in receptacles, stems, and roots, but lower levels in stamens and petals. Salt, drought, and cold stress treatments induced upregulation of GhMLO family members, with most genes showing increased expression over time. RT-qPCR analysis validated that five candidate GhMLO genes were significantly upregulated under salt stress. In summary, this study provides a comprehensive genome-wide characterization of the GhMLO gene family, elucidating their phylogenetic relationships and expression dynamics, which establishes a theoretical basis for identifying key regulatory genes involved in abiotic stress responses and offers novel genetic resources for improving stress tolerance in cotton molecular breeding.

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.