**5.2 Molecular basis of RFS resistance**

Since many rice cultivars with high RFS resistance or high susceptibility have been identified, comparative transcriptome analysis is a promising method to mine resistance- or susceptibility-related genes in rice. For instance, time-course RNAseq was carried out on susceptible cultivar LYP9 and resistant cultivar IR28 upon *V. virens* infection [62]. Data analysis revealed that many defense-related genes were only up-regulated in the resistant cultivar IR28, but not in LYP9. Particularly, phytoalexin biosynthetic pathway genes such as *OsCPS2*, *OsMAS*, and *OsKSL11* were significantly induced in IR28 at early infection stages, indicating that phytoalexins may contribute to rice resistance against RFS. *PR* family genes, such as β-1,3 glucanase and chitinase genes, were specifically up-regulated in IR28, while generally down-regulated in LYP9. Moreover, a chitinase gene cluster was found close to a RFS resistance QTL on chromosome 11 [71], and nine genes in this cluster were

activated by *V. virens* infection. These data suggest that chitinase genes are potential candidates of RFS resistance. In addition, genes encoding receptor-like kinases and WRKY transcription factors may also play roles in RFS resistance. Interestingly, the resistant cultivar IR28 seemed to suppress *V. virens* genes that are associated with pathogenicity and fungal reproduction [62]. Another comparative transcriptome study demonstrated that peroxidase and flavin-containing monooxygenase genes, and genes involved in hormone metabolism were regulated differently in resistant and susceptible cultivars in response to *V. virens* infection [61].

Accumulation of H2O2 is a typical plant basal defense fighting against pathogen infections [73]. During a compatible interaction between rice and *V. virens*, obvious H2O2 accumulation was detected on the lemma and the palea of infected spikelet. H2O2 also enriched in the anthers, stamen filaments, and lodicules of the infected spikelets [74]. However, it needs to be further investigated whether H2O2 accumulation pattern is different between resistant and susceptible rice cultivars upon *V. virens* infection. A preliminary study described that higher contents of lignin and polyphenolic compounds were detected in spikelets of resistant rice variety Shuijing 3 than in those of susceptible variety 9522 [75], suggesting the role of these secondary metabolites in RFS resistance. To engineer rice resistant to RFS, an elicitor gene *hrf1* from *Xanthomonas oryzae* pv. *oryzae* was ectopically expressed in R109, which is susceptible to RFS. Artificial inoculation and natural infection both supported that *hrf1* conferred high resistance to the RFS pathogen, presumably through enhancing the expression of defense-related genes, including *OsPR1a*, *OsPR1b,* and *PAL* [76].

Based on the current findings that *V. virens* possesses intercellular infection strategy and biotrophic life style, and that resistant rice cultivars show up-regulation of pathogenesis-related genes and accumulation of secondary metabolites upon infection, basal defense of rice should play a dominant role in resistance against *V. virens*.
