Genome-wide analysis of the HDAC gene family in Pyrus betulifolia and functional validation of PcHDAC5 and PcHDT1.2 in Pyrus calleryana seed dormancy release.

Histone deacetylation, catalyzed by histone deacetylases (HDACs), is a core epigenetic regulatory mechanism in plants. However, no systematic characterization of the HDAC gene family has been reported in pear (Pyrus spp.), a globally important temperate fruit crop. In this study, we performed genome-wide identification and functional characterization of HDAC genes in pear, with a specific focus on their regulatory roles in seed dormancy release. We identified 22 PbHDAC genes from the genome of Pyrus betulifolia Bunge, which were classified into three conserved subfamilies. Evolutionary analysis confirmed that all PbHDAC genes have undergone strong purifying selection. Transcriptome profiling of Pyrus calleryana Decne seeds identified seven PcHDAC genes differentially expressed during seed dormancy release, and quantitative real-time PCR (qRT-PCR) verified that only PcHDAC5 and PcHDT1.2 showed consistent significant differential expression throughout this process. Using an optimized antisense oligonucleotide (as-ODN)-mediated silencing system tailored for hard-coated pear seeds, we demonstrated that PcHDT1.2 and PcHDAC5 act as negative and positive regulators of seed dormancy release, respectively. Further experiments revealed that knockdown of these two genes altered the contents of abscisic acid (ABA) and indole-3-acetic acid (IAA). Collectively, this study not only fills the long-standing gap in systematic HDAC family research in pear, but also provides a robust technical workflow for functional gene validation in hard-coated seeds, with important implications for pear rootstock breeding and seed germination regulation.