A viroid‐derived small interfering RNA targets bHLH transcription factor MdPIF1 to regulate anthocyanin biosynthesis in Malus domestica

• Published in: Plant, cell and environment Vol. 47; no. 12; pp. 4664 - 4682
• Main Authors: Zhang, Zhenlu, Li, Zhao‐Yang, Zhang, Fu‐Jun, Zheng, Peng‐Fei, Ma, Ning, Li, Lianzhen, Li, Haojian, Sun, Ping, Zhang, Shuai, Wang, Xiao‐Fei, Lu, Xiao‐Yan, You, Chun‐Xiang
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.12.2024
• Subjects: anthocyanin biosynthesis; Anthocyanins; Anthocyanins - biosynthesis; Anthocyanins - metabolism; Apple dimple fruit viroid; apple fruit coloration; Apples; Basic Helix-Loop-Helix Transcription Factors - genetics; Basic Helix-Loop-Helix Transcription Factors - metabolism; Biosynthesis; callus; color; Coloration; Dimpling; environment; Fruit - genetics; Fruit - metabolism; Fruit - virology; fruit color; Fruits; Gene expression; Gene Expression Regulation, Plant; Injection; Malus - genetics; Malus - metabolism; Malus - virology; Malus domestica; MdPIF1; microRNA; miRNA; Plant Proteins - genetics; Plant Proteins - metabolism; Promoter Regions, Genetic - genetics; Ribonucleic acid; RNA; RNA interfering; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; siRNA; Transcription factors; transcriptional regulation; Viroids; Viroids - genetics; Viroids - physiology; viroid‐derived small RNAs; MdPIF1; RNA interfering; apple fruit coloration; transcriptional regulation; anthocyanin biosynthesis; viroid‐derived small RNAs
• DOI: 10.1111/pce.15051
• ISSN: 0140-7791; 1365-3040

Fruit colour is a critical determinant for the appearance quality and commercial value of apple fruits. Viroid‐induced dapple symptom severely affects the fruit coloration, however, the underlying mechanism remains unknown. In this study, we identified an apple dimple fruit viroid (ADFVd)‐derived small interfering RNA, named vsiR693, which targeted the mRNA coding for a bHLH transcription factor MdPIF1 (PHYTOCHROME‐INTERACTING FACTOR 1) to regulate anthocyanin biosynthesis in apple. 5’ RLM‐RACE and artificial microRNA transient expression system proved that vsiR693 directly targeted the mRNA of MdPIF1 for cleavage. MdPIF1 positively regulated anthocyanin biosynthesis in both apple calli and fruits, and it directly bound to G‐box element in the promoter of MdPAL and MdF3H, two anthocyanin biosynthetic genes, to promote their transcription. Expression of vsiR693 negatively regulated anthocyanin biosynthesis in both apple calli and fruits. Furthermore, co‐expression of vsiR693 and MdPIF1 suppressed MdPIF1‐promoted anthocyanin biosynthesis in apple fruits. Infiltration of ADFVd infectious clone suppressed coloration surrounding the injection sites in apple fruits, while a mutated version of ADFVd, in which the vsiR693 producing region was mutated, failed to repress fruit coloration around the injection sites. These data provide evidence that a viroid‐derived small interfering RNA targets host transcription factor to regulate anthocyanin biosynthesis in apple. Summary Statement Our work identifies an apple dimple fruit viroid‐derived small RNA that mediating the cleavage of mRNA of a bHLH transcription factor MdPIF1, a positive regulator in anthocyanin biosynthesis, resulting in decreased synthesis and accumulation of anthocyanin in apple (Malus domestica) fruits.