Identification of miRNA-Target Gene Pairs Responsive to Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles.

wilt () of cucumber ( L.) caused by f. sp. (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar 'Rijiecheng', which is resistant to . The integrated analysis identified -responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that (), which is targeted by , and (), (), and (), which are targeted by , are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that -, -, - and - regulate cucumber defenses against , and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to .