Characterization of GhHD2A-D05, an HD2-type histone deacetylase, as a positive regulator in cotton drought response

Drought is a major abiotic stress limiting cotton production. Identifying key drought-responsive genes and elucidating their regulatory mechanisms are of great scientific and practical value for developing drought-tolerant cotton germplasm and cultivars. HD2-type histone deacetylases are epigenetic regulators unique to plants that are essential for plant responses to abiotic stressors. In this study, we identified a HD2A family gene in Gossypium hirsutum , GhHD2A-D05 , whose expression is significantly induced by drought, polyethylene glycol (PEG), and abscisic acid (ABA) treatments. Functional analysis revealed that silencing GhHD2A-D05 via virus-induced gene silencing (VIGS) markedly reduced drought tolerance in cotton plants. Under drought stress(DS), silenced plants exhibited decreased activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), reduced proline (PRO) accumulation, lower leaf relative water content (RWC), and elevated levels of malondialdehyde (MDA). Conversely, overexpression (OE) of GhHD2A-D05 in Arabidopsis thaliana enhanced drought tolerance. Transcriptome analysis showed that silencing GhHD2A-D05 resulted in 2446 differentially expressed genes (DEGs) under drought conditions.The KEGG enrichment analysis indicated that these genes were mainly linked to "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", and "Tryptophan metabolism". Notably, expression of multiple genes implicated in ABA biosynthesis (e.g., NCEDs) and signaling (e.g., PP2Cs, ABFs) was significantly altered in silenced plants. Collectively, our findings suggest that GhHD2A-D05 positively regulates cotton drought response, potentially through modulating ABA biosynthesis and signaling pathways, along with other metabolic processes, providing a novel candidate gene and theoretical foundation for molecular breeding of drought-tolerant cotton. • GhHD2A-D05 (novel HD2A-type histone deacetylase) is a new drought-responsive epigenetic modulator identified from cotton. • GhHD2A-D05 positively regulates drought tolerance via antioxidants, osmotic balance and membrane stability. • GhHD2A-D05 modulates cotton drought response via ABA signaling and phenylpropane/tryptophan metabolism; silencing alters key ABA genes (NCEDs, PP2Cs, ABFs).