SET-domain group histone methyltransferases (SDGs) are known to play crucial roles in plant responses to abiotic stress. However, their specific function in cotton’s response to drought stress has not been well understood. This study conducted a comprehensive analysis of the SDG gene family in Gossypium hirsutum, identifying a total of 82 SDG genes. An evolutionary analysis revealed that the SDG gene family can be divided into eight subgroups. The expression analysis shows that some GhSDG genes are preferentially expressed in specific tissues, indicating their involvement in cotton growth and development. The transcription level of some GhSDG genes is induced by PEG, with GhSDG59 showing significant upregulation upon polyethylene glycol (PEG) treatment. Quantitative polymerase chain reaction (qPCR) analysis showed that the accumulation of transcripts of the GhSDG59 gene was significantly upregulated under drought stress. Further functional studies using virus-induced gene silencing (VIGS) revealed that silencing GhSDG59 reduced cotton tolerance to drought stress. Under drought conditions, the proline content, superoxide dismutase (SOD) and peroxidase (POD) enzyme activities in the GhSDG59-silenced plants were significantly lower than in the control plants, while the malondialdehyde (MDA) content was significantly higher. Transcriptome sequencing showed that silencing the GhSDG59 gene led to significant changes in the expression levels of 1156 genes. The KEGG enrichment analysis revealed that these differentially expressed genes (DEGs) were mainly enriched in the carbon metabolism and the starch and sucrose metabolism pathways. The functional annotation analysis identified known drought-responsive genes, such as ERF, CIPK, and WRKY, among these DEGs. This indicates that GhSDG59 is involved in the drought-stress response in cotton by affecting the expression of genes related to the carbon metabolism and the starch and sucrose metabolism pathways, as well as known drought-responsive genes. This analysis provides valuable information for the functional genomic study of SDGs and highlights potential beneficial genes for genetic improvement and breeding in cotton.

ABA2 encodes a short-chain dehydrogenase/reductase involved in the regulation of abscisic acid (ABA) biosynthesis and plays a crucial role in plant responses to salt stress. To explore the function of GhABA2 in cotton salt tolerance, we conducted bioinformatic analyses, gene overexpression, and virus-induced gene silencing (VIGS) experiments. Bioinformatic examination revealed that the promoter region of the GhABA2 gene contains multiple cis -acting elements, including those responsive to ABA, light, and various stress signals. Overexpression of GhABA2 in Arabidopsis resulted in significantly increased seed germination rate, root length, leaf relative water content (RWC), catalase (CAT) activity, peroxidase (POD) activity, and proline (Pro) content under salt stress conditions, while malondialdehyde (MDA) content was markedly reduced. Conversely, silencing GhABA2 gene in cotton via virus-induced gene silencing (VIGS) led to significant decreases in ABA content, RWC, superoxide dismutase (SOD) activity, POD activity, and Pro content, along with a significant increase in MDA content. These findings provide important insights into the mechanism of GhABA2 in mediating cotton salt stress response and highlight its potential as a genetic target for breeding of salt-tolerant cotton varieties.