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Background   APETALA2 -like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target  euAP2  genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target  AP2  genes remain largely unknown in  Brassica napus  ( B. napus ).    Results  In this study, 19  euAP2  and four miR172 genes were identified in the  B. napus  genome. A sequence analysis suggested that 17  euAP2  genes were targeted by Bna-miR172 in the 3′ coding region.  EuAP2 s were classified into five major groups in  B.napus . This classification was consistent with the exon-intron structure and motif organization. An analysis of the nonsynonymous and synonymous substitution rates revealed that the  euAP2  genes had gone through purifying selection. Whole genome duplication (WGD) or segmental duplication events played a major role in the expansion of the  euAP2  gene family. A cis-regulatory element (CRE) analysis suggested that the  euAP2 s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. Expression analysis of the miR172-targeted  euAP2s  in nine different tissues showed diverse spatiotemporal expression patterns. Most  euAP2  genes were highly expressed in the floral organs, suggesting their specific functions in flower development.  BnaAP2–1 ,  BnaAP2–5  and  BnaTOE1–2  had higher expression levels in late-flowering material than early-flowering material based on RNA-seq and qRT-PCR, indicating that they may act as floral suppressors.    Conclusions  Overall, analyses of the evolution, structure, tissue specificity and expression of the  euAP2  genes were peformed in  B.napus . Based on the RNA-seq and experimental data,  euAP2  may be involved in flower development. Three  euAP2  genes ( BnaAP2–1 ,  BnaAP2–5  and  BnaTOE1–2 ) might be regarded as floral suppressors. The results of this study provide insights for further functional characterization of the miR172 / euAP2  module in  B.napus .    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1936-2) contains supplementary material, which is available to authorized users.

Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development