miRNA expression profiling reveals the regulators of kiwifruit response to Botrytis cinerea

Gray mold caused by Botrytis cinerea leads to widespread rot and substantial economic losses in kiwifruit production. However, the molecular basis of compatible host–pathogen interactions remains unestablished. We adopted a next-generation sequencing approach to determine the differential expression of miRNAs during B. cinerea-induced stress in kiwifruit. Nineteen known and 325 novel miRNAs, of which 155 were differentially expressed, showed at least 1.5-fold changes in expression, with a majority being upregulated. Expression of miRNAs most pertinent to the kiwifruit response to B. cinerea was concentrated mainly in the first 3 days post-infection. Target gene prediction based on database screens revealed 2156, 2864, and 288 targets of 155 miRNAs differentially expressed on post-infection days 1, 2, and 3, respectively. GO and KEGG enrichment-based categorization of gene functions revealed significant associations between these genes and Plant–pathogen interaction; secondary-like Steroid, Phenylpropanoid, and Flavonoid biosynthesis; and Plant hormone signal transduction pathways. We thus identified key miRNA regulators of the B. cinerea stress response in kiwifruit and a putative subset of genes that are potentially post-transcriptionally silenced during infection. These findings could provide new insights regarding the regulatory mechanisms underlying disease resistance in kiwifruit and contribute genetic resources for molecular breeding of disease-resistant kiwifruit.