The role of ncRNAs in the interaction between root-knot nematode and rice

In this study, the involvement of non-coding RNAs (ncRNAs) in the infection of rice (Oryza sativa) by the root-knot nematode (Meloidogyne graminicola) is being investigated. Meloidogyne graminicola, is a major economic threat to worldwide rice production. By performing small and total RNA sequencing on healthy roots and galls at 3 days post infection, we identified 15 differentially expressed miRNAs and thousands of lncRNAs likely to play a role in the infection process. Putative targets for the miRNAs were predicted and cross referenced with the total RNA dataset. The expression profile of differentially expressed targets was validated by RT-qPCR. To ensure the quality of the validation, several candidate reference miRNAs were tested for expression stability and the two stablest transcripts were chosen. Among the predicted targets is a gene encoding ascorbate oxidase, which could play a role in the plant defense response. Furthermore, two miRNAs are putatively involved in a miRNA-decoy-target system. Clustering analysis revealed that hundreds of differentially expressed lncRNAs are clustered together with differentially expressed protein coding genes, suggesting potential in cis expression regulation. Furthermore, overexpression lines of four differentially expressed miRNAs are currently tested in infection assays. This research will contribute to a deeper understanding of ncRNA involvement in rice immunity which, in turn, may contribute to new nematode control strategies