The tomato microRNA miRcn1 acts as a positive regulator of resistance to nematode infection by targeting the cytokinin response factor SlCRF9

Root-knot nematodes (RKN; Meloidogyne spp) are plant endoparasites with a broad host range which cause huge crop losses globally. MicroRNAs (miRNAs) play important roles in plant responses to abiotic and biotic stresses by silencing the transcriptional and post-transcriptional expression of genes. In this study, miRNAs of RKN-infected and -uninfected roots of the susceptible tomato ( Solanum lycopersicum ) cultivar Moneymaker were subjected to high-throughput sequencing. A novel miRNA (named as miRcn1) was down-regulated upon RKN infection, while the transcripts of its predicted target, the cytokinin response factor 9 ( SlCRF9 ), increased. The interaction of miRcn1 with SlCRF9 was confirmed by qRT-PCR and Agrobacterium-mediated transient co-expression in Nicotiana benthamiana . Tomato plants overexpressing miRcn1 showed reduced SlCRF9 transcript levels and enhanced resistance to RKN. In contrast, tomato plants overexpressing SlCRF9 were more susceptible to RKN infection and exhibited growth retardation. A jasmonic acid (JA)-dependent gene, PDF1.2 , was upregulated and downregulated in miRcn1- and SlCRF9 -overexpressing lines, respectively. Taken together, these results demonstrate that miRcn1 positively regulates tomato resistance to M. incognita infection by silencing SlCRF9 expression.