Genome-Wide Identification of the Zinc Finger-Homeodomain (<i>ZF-HD</i>) Gene Family and Their Response to Cold Stress in <i>Rosa chinensis</i>

<h4>Background</h4>The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for <i>Rosa chinensis</i>.<h4>Methods</h4>In this study, we performed a comprehensive genome-wide identification and analysis of <i>RcZF-HD</i> genes in <i>R. chinensis</i> using bioinformatics approaches. Nine <i>RcZF-HD</i> loci were mined from the rose genome and comprehensively profiled for physicochemical parameters, phylogenetic affiliations, chromosomal positions, exon-intron architectures, conserved motifs, and spatiotemporal expression landscapes.<h4>Results</h4>The results showed that <i>RcZF-HD</i> genes were unevenly distributed across four chromosomes (Chr2, Chr4, Chr6, and Chr7), with tandem duplication events detected on chromosomes 2 and 7, suggesting their contribution to gene family expansion. Maximum-likelihood phylogeny placed RcZF-HD proteins within nine well-supported sub-clades alongside <i>Arabidopsis</i> orthologs, implying both evolutionary conservation and lineage-specific divergence. All members retain canonical zinc-finger domains, yet acquire unique motif signatures predictive of functional specialization. Gene structure analysis revealed considerable diversity in exon-intron organization. Expression profiling across six different tissues (root, stem, leaf, bud, flower, and fruit) demonstrated remarkable tissue-specific expression patterns. Notably, <i>RchiOBHm_Chr2g0168531</i> exhibited extremely high expression in stem tissue, while <i>RchiOBHm_Chr7g0181371</i> showed preferential expression in flower tissue, suggesting specialized roles in stem development and floral organ formation, respectively. The cold-stress challenge of 'Old Blush' petals further disclosed pronounced up-regulation of seven <i>RcZF-HD</i> genes, attesting to their critical contribution to low-temperature tolerance.<h4>Conclusions</h4>Integrative analyses furnish a multidimensional blueprint of the rose <i>RcZF-HD</i> repertoire, providing molecular landmarks for future functional dissection and ornamental trait engineering.