Genome-Wide Identification and Expression Profiling of HD-ZIP Transcription Factor Family in Poncirus trifoliata Under Phytohormone and Abiotic Stress Treatments

In this study, we identified 34 HD-ZIP genes at the genome-wide level in P. trifoliata (Poncirus trifoliata (L.) Raf.), and conducted comprehensive bioinformatic analyses. The expression profiles of PtrHB genes in response to six phytohormones (ABA, SA, JA, BR, ETH, GA) and two abiotic stresses (dehydration, cold) were further determined. Phylogenetic analysis assigned all PtrHB proteins to four distinct subfamilies (I–IV) with highly conserved domain compositions, in line with the established classification system in Arabidopsis thaliana. Segmental duplication was revealed as the primary driver of PtrHB family expansion, whereas three tandem duplication events were also detected. Promoter cis-element profiling revealed subfamily-specific distribution of hormone- and stress-responsive elements. Several candidate genes with prominent stimulus-specific responses were highlighted, including PtrHB32 (strongly induced by dehydration, cold and ABA), PtrHB15 (JA-responsive) and PtrHB16 (SA-responsive). Collectively, this study provides the first systematic genome-wide analysis of the HD-ZIP transcription factor family in P. trifoliata, and offers valuable insights into the evolutionary expansion and functional divergence of this family. Our results also lay a theoretical basis for functional validation of candidate stress-regulatory genes and for molecular breeding of stress-tolerant citrus rootstocks.