MicroRNAs (miRNAs) play an important regulatory role in plant growth and development, as well as in response to multiple stresses. In recent years, multiple studies have shown that miRNAs participate in regulating diverse aspects of the plant-pathogen interactions, but little is known about the potential existence and functional roles of pathogen-responsive miRNAs in apple (Malus × domestica Borkh.). Here, we identified pathogen-responsive miRNAs in apple leaves challenged by Alternaria alternata apple pathotype (AAAP). These AAAP-responsive miRNAs were classified into 41 families and predicted to target 673 genes, including multiple R genes and transcription factors, such as LRR, RPK2, LACCASE, and MYB, among others. A follow-up analysis revealed that some of the AAAP-responsive miRNAs and their predicted targets exhibited differential expression patterns in the disease-susceptible vs. disease-resistant apple cultivars, i.e. ‘Starking Delicious’ vs. ‘Jonathon’, indicating that these miRNAs are involved in the regulation of apple resistance to AAAP infection. Then, we focused specifically on a potential negative regulatory impact of mdm-miR390a on disease resistance and predicted the impact may result from targeting and inhibiting the expression of the MdRPK2 and MdLRR8 genes, which was confirmed experimentally in both Agrobacterium co-infiltration assays in tobacco (Nicotiana benthamiana) and apple (Malus × domestica ‘Gala’). The results showed that overexpression of mdm-miR390a enhanced the sensitivity to AAAP infection, and overexpression of MdLRR8 or MdRPK2 improved the resistance to AAAP while co-expression with mdm-miR390a counteracted the resistance. Above all, beyond presenting a large data resource for studies of miRNA species and miRNA-based regulation mechanisms in tree fruit, our study uncovered a fascinating case wherein a fungus-induced plant-genome-encoded miRNA apparently increases the susceptibility of the plant host to fungal infection via a post-transcriptional R-gene-knockdown mechanism.

MicroRNAs (miRNAs) 在植物生长发育以及对多种胁迫的响应中发挥着重要的调节作用。近年来，多项研究表明 miRNAs 参与调节植物-病原体相互作用的各个方面，但对病原体响应 miRNAs 在苹果 ( Malus ×domestica Borkh . ) 中的潜在存在和功能作用知之甚少。在这里，我们确定病原体-通过挑战苹果叶响应的miRNA链格孢苹果致病型（AAAP）。这些 AAAP 响应的 miRNA 被分为 41 个家族，并预测靶向 673 个基因，包括多个R基因和转录因子，如LRR、RPK2、LACCASE，和MYB等。后续分析显示，一些 AAAP 响应 miRNA 及其预测靶标在疾病易感与抗病苹果栽培品种中表现出差异表达模式，即“Starking Delicious”与“Jonathon”，表明这些 miRNAs参与调节苹果对 AAAP 感染的抗性。然后，我们特别关注 mdm-miR390a 对疾病抗性的潜在负面调节影响，并预测该影响可能源于靶向和抑制MdRPK2和MdLRR8基因的表达，这在烟草中的农杆菌共浸润试验中得到了实验证实(本氏烟草) 和苹果 ( Malus ×domestica 'Gala')。结果表明，mdm-miR390a的过表达增强了对AAAP感染的敏感性，MdLRR8或MdRPK2的过表达提高了对AAAP的抗性，而与mdm-miR390a的共表达则抵消了抗性。最重要的是，除了提供大量数据资源用于研究树果中 miRNA 种类和基于 miRNA 的调控机制之外，我们的研究还发现了一个引人入胜的案例，其中真菌诱导的植物基因组编码的 miRNA 显然增加了植物宿主对通过转录后R-基因敲低机制进行真菌感染。