Genome‐wide analysis of the AP2/ERF gene family in <i>Rheum officinale</i> Baill.: Evolution and expression profiling during plant development, abiotic stresses, and exogenous hormone responses

The APETALA2/ethylene-responsive factor (AP2/ERF) superfamily plays a central role in plant metabolism, stress responses, and hormone signaling. Rheum officinale Baill. is an important traditional medicinal plant whose roots and rhizomes are rich in anthraquinones and other secondary metabolites. However, the regulatory mechanisms underlying its development and secondary metabolism remain unclear, and systematic analyses of its AP2/ERF family are lacking. This study aimed to characterize the genomic features, expression patterns, and potential functions of the AP2/ERF family in R. officinale. A total of 167 RoAP2/ERF genes were identified, unevenly distributed across 11 chromosomes. Gene family expansion was mainly driven by segmental and tandem duplications, with extensive collinearity observed between R. officinale and related species. Phylogenetic, conserved domain, gene structure, and motif analyses classified these genes into five subfamilies (ERF, dehydration reaction element binding factor; AP2, related to abscisic acid insensitive 3/viviparous 1; and Soloist), with similar sequence characteristics within each subfamily. RNA-seq analysis revealed tissue-specific expression patterns, with Cluster 5 genes preferentially expressed in roots and rhizomes. RT-qPCR of 18 representative genes confirmed their involvement in various signaling pathways. RoERF065 and RoERF079 were exclusively nuclear-localized and strongly responsive to stress and hormone treatments. Functional assays indicated that RoERF079 acts as a C-terminal-dependent transcriptional activator, whereas RoERF065 may function as a repressor due to two EAR motifs. These genes may regulate root and rhizome development and secondary metabolism in R. officinale. This study provides a basis for elucidating the molecular mechanisms of organ development and bioactive compound biosynthesis and identifies candidate genes for molecular breeding.