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Background  The AP2/ERFs belong to a large family of transcription factors in plants. The AP2/ERF gene family has been identified as a key player involved in both biotic and abiotic stress responses in plants, however, no comprehensive study has yet been carried out on the AP2/ERF gene family in rose ( Rosa  sp.), the most important ornamental crop worldwide.    Results  The present study comprises a genome-wide analysis of the AP2/ERF family genes ( RcERFs ) in the rose, involving their identification, gene structure, phylogenetic relationship, chromosome localization, collinearity analysis, as well as their expression patterns. Throughout the phylogenetic analysis, a total of 131  AP2/ERF  genes in the rose genome were divided into 5 subgroups. The  RcERFs  are distributed over all the seven chromosomes of the rose, and genome duplication may have played a key role in their duplication. Furthermore, Ka/Ks analysis indicated that the duplicated  RcERF  genes often undergo purification selection with limited functional differentiation. Gene expression analysis revealed that 23  RcERFs  were induced by infection of the necrotrophic fungal pathogen  Botrytis cinerea . Presumably, these  RcERFs  are candidate genes which can react to the rose’s resistance against  Botrytis cinerea  infection. By using virus-induced gene silencing, we confirmed that  RcERF099  is an important regulator involved in the  B.cinerea  resistance in the rose petal.    Conclusion  Overall, our results conclude the necessity for further study of the AP2/ERF gene family in rose, and promote their potential application in improving the rose when subjected to biological stress.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02740-6.

Global analysis of the AP2/ERF gene family in rose (Rosa chinensis) genome unveils the role of RcERF099 in Botrytis resistance