Genome-wide analysis of auxin response factor (ARF) genes and functional identification of MdARF2 reveals the involvement in the regulation of anthocyanin accumulation in apple

Auxin response factors (ARFs) mediate auxin response gene transcription by directly binding with AuxREs. However, whether ARF family genes involved in anthocyanin accumulation in apple is largely unexplored. In this study, thirty-three MdARF family members were identified in the apple (Malus x domestica) genome (HFTH1 Whole Genome v1.0) based on the sequence similarity with ARF family members ofArabidopsis. Phylogenetic analysis revealed that thirty-three MdARF members were clustered into Class I, Class II and Class III. Functional domain analysis showed that MdARF proteins have some typical domains such as B3-like DNA-binding domain and Auxin_resp domain, as well as motif III and motif IV. Chromosome localisation analysis demonstrated that apple ARF members were widely distributed in the genome. Among theseMdARFgenes,MdARF2was significantly correlated with anthocyanin variation according to extracting expression profiles from published RNA-seq data. Further functional identification in apple calli suggested that MdARF2 functions as a transcriptional repressor of anthocyanin biosynthesis. These findings provide evidence that MdARF family members play a role in the regulation of anthocyanin accumulation in apple.

Automated summary

This study identified 33 MdARF family members in the genome of apple and found MdARF2 to have a significant correlation with anthocyanin variation. Functional identification suggested that MdARF2 acts as a transcriptional repressor of anthocyanin biosynthesis in apple, indicating the role of MdARF family members in the regulation of anthocyanin accumulation.