Evaluation of reference genes and expression of key genes involved in the isoprenoid metabolic pathway of rice leaves after infection by the Southern rice black-streaked dwarf virus.

The Southern rice black-streaked dwarf virus (SRBSDV), a novel Fijivirus, poses a major threat to rice production in East Asia. Analysis of the gene expression of SRBSDV-infected rice plants may reveal the molecular basis of interactions between the virus, its vector and rice plants. Reliable reference genes are required for accurate qRT-PCR analysis. However, no reliable, valid reference genes for examining gene expression in SRBSDV-infected rice plants have so far been identified. We examined the expression of eight candidate reference genes in the leaves of SRBSDV-infected, and healthy, rice plants at different points in time after virus inoculation. We used four dedicated algorithms, geNorm, BestKeeper, NormFinder and RefFinder, to evaluate the performance of these candidate genes. The RefFinder results indicate that 18S, EF1α and UBQ10 are suitable reference genes. In addition, we used these three reference genes to analyze the expression of key genes involved in the isoprenoid metabolic pathway in rice leaves after infection by SRBSDV. The results of this analysis reveal that SRBSDV may suppress the production of the rice plant volatiles that attract natural enemies of its vector Sogatella furcifera, thereby increasing the likelihood of pathogen transmission.