Identification of histone modification genes in strawberry reveals the role of the histone deacetylase FaHDT in fruit ripening

Background Histone modifications (HMs) play pivotal roles in plant growth and development. However, a comprehensive analysis of the HMs genes and their specific functions in strawberry fruit ripening is still lacking. Results In this study, a genome-wide identification of HMs genes was performed in the diploid strawberry ( Fragaria × vesca). Phylogenetic relationships, chromosomal locations, synteny, and expression patterns were analyzed. Furthermore, the functions of histone deacetylases (HDACs) FaHDT1 and FaHDT2 were characterized through transient RNAi assays in octoploid strawberry ( Fragaria × ananssa ) fruits. A total of 139 HMs genes were identified and classified into 11 subfamilies. Phylogenetic analysis revealed conserved evolutionary relationships among strawberry, Arabidopsis , and tomato. Expression profiling and subcellular localization indicated that FaHDT1 and FaHDT2 were significantly upregulated during fruit ripening and localized specifically in the nucleus. Notably, functional analysis demonstrated that FaHDT-mediated histone deacetylation participates in the regulation of fruit ripening. Transient RNAi silencing of FaHDT1 or FaHDT2 significantly delayed fruit ripening, resulting in increased fruit firmness and reduced accumulation of anthocyanins and volatile compounds. Conclusion This study provides the first comprehensive bioinformatic analysis of the HMs gene family in strawberry. The results confirm that FaHDT1 and FaHDT2 act as positive regulators in the strawberry fruit ripening process through histone deacetylation, which provides novel epigenetic insights into the non-climacteric fruit ripening process.