MIR396d-p3 Negatively Regulates Apple Resistance to Colletotrichum gloeosporioides via MdUGT89A2 and MdRGA3

Apple (Malus domestica) is an economically important fruit crop, but its production is affected by Glomerella leaf spot, a devastating disease caused by the fungal pathogen Colletotrichum gloeosporioides. MicroRNA (miRNA) is a kind of non-coding RNA that plays an important role in the process of plant–pathogen interactions. However, little is known about the miRNAs that influence apple resistance against C. gloeosporioides. A novel miRNA, MIR396d-p3, was identified through small RNA sequencing (sRNA-seq). Functional analyses revealed that MIR396d-p3 negatively regulates apple resistance to C. gloeosporioides. In addition, MdUGT89A2 and MdRGA3 were confirmed as targets of MIR396d-p3 using 5′ RACE and heterologous expression assays. We further found that overexpressing MdUGT89A2 and MdRGA3 induce apple disease resistance to C. gloeosporioides, while silencing of MdUGT89A2 and MdRGA3 reduces resistance to C. gloeosporioides. These results indicate that MIR396d-p3 plays a role in the response to the infection of C. gloeosporioides through regulating the expressions of MdUGT89A2 and MdRGA3. This research provides a new perspective on the interaction between apples and C. gloeosporioides and offers possible targets for resistance breeding.