Genome-wide identification of the histone gene family in foxtail millet (Setaria italica) and analysis of its expression pattern in response to abiotic stress

Histones are central to chromatin structure and function and play critical roles in gene regulation and environmental adaptation. This study presents a genome-wide analysis of the histone gene family in foxtail millet (Setaria italica), a stress-resistant cereal crop. We identified a total of 55 histone genes (H1, H2A, H2B, H3, and H4) and revealed that family expansion, driven primarily by segmental duplication events, has been under strong purifying selection. Phylogenetic analysis revealed that distinct evolutionary paths between core histones and the linker histones H1, H3 and H4 were highly conserved, whereas H2A and H1 presented greater lineage-specific diversification. Synteny analysis further demonstrated that the conservation of histone genes is strongly correlated with evolutionary distance among species. Promoter analysis revealed numerous cis-acting elements related to abiotic stress and hormone responsiveness. Expression profiling indicated that most histone genes were highly expressed in meristematic tissues, underscoring their core function in cell division. More importantly, under saline-alkali and cold stress, we identified a set of co-upregulated histone genes (e.g., SiH2A.5, SiH4.10, and SiH4.11), which may be candidate genes associated with saline-alkali and cold stress response. This study provides a foundation and insights into the foxtail millet histone family and its potential role in stress response.