MicroRNA-mediated regulation of R-genes: Lessons from model systems
Plants have evolved an array of resistance genetic mechanisms to cope with pathogens and herbivores. Modern cultivars are being developed by pyramiding multiple R-genes as well as genes involved in quantitative mechanisms to avoid substantial economic loss to crop productivity. However, it has been shown that constitutive expression of R-genes often imposes high fitness costs that can have deleterious consequences to plant growth and development. Therefore, the expression of R-genes must be tightly regulated and activated in the right spatial and temporal manner.
Emerging evidence suggested that the miRNAs and secondary siRNA play important roles in the regulation of R-gene expression by silencing the immune-response receptors in absence of pathogens. This mechanism is important in the stabilization of the basal transcript levels in order to limit the fitness costs of an overactive immune response (Figure 2). Plants have evolved specific miRNAs that function in targeting the conserved domains in R-genes. The miR472 was the first miRNA known to be directly targeting the CC-NBS-LRRs domain-containing immune receptor genes in Arabidopsis (Lu et al. 2006). Since its discovery, many other miRNAs involved in R-gene regulation have been described that optimizes the defense-fitness trade-off in plants. For example, the sequence-specific cleavage of the TIR-NB-LRR immune receptor of N gene transcripts that conditions resistance to tobacco mosaic virus (TMV) were shown to be mediated by nta-miR6019 andnta-miR6020 in Solanaceae family (Li et al. 2012). The miR482/2118 super-family targeting NB-LRR genes have also been well characterized in tomato and its prime importance in the regulation of immune response has been well justified (Shivaprasadet al. 2012). Recently, Osa-miR1876 has been shown to epigenetically regulate the expression of NBS8R gene encoding a NB-ARC domain protein that confers resistance to X. oryzae in rice (Jiang et al. 2020).
Apart from the direct targeting of NLRs, miRNAs have also been shown to indirectly regulate R-genes via targeting the genes that co-expressed with R-genes (Wang & Galili 2019). The NBS-LRRs which are not primarily recognized by miRNA triggers the production of a phased array (in a sequential, head-to-tail manner, according to the miRNA cleavage site) of 21-nt secondary small-interfering RNAs (phasiRNAs) to amplify the silencing effects (Fei, Xia & Meyers 2013). These phasiRNAs are act intrans manner to silence the addition R-gene transcripts. The fine-tuning of NBS-LRR protein expression by phasiRNA inhibits the constitutive expressions R-genes, which is potentially detrimental for plant growth. In the model legume Medicago truncatula, 22-nt miRNAs including miR2275 , miR2109 , and miR2118 have been shown to trigger the production of phasiRNA that are specifically associated with the regulation of NBS-LRR immune receptors (Zhaiet al. 2011; Fei, Li, Teng & Meyers 2015). These miRNAs are highly conserved in both legumes and non-legume plant species.
In rice, numerous phasiRNAs are preferentially produced and accumulated in reproductive tissues, particularly anthers, suggesting possible roles in reproductive development (Johnson et al. 2009; Song et al. 2012). The rice Agronaute protein MEL1 (MEIOSIS ARRESTED AT LEPTOTENE 1 ) plays a central role in gametogenesis. Loss-of-function mutation in MEL1 impedes chromosome condensation during early meiosis, causing male sterility with aberrant vacuolated pollen mother cells. The Osa-miR2118 targets over 700 long-intergenic noncoding RNAs (lincRNAs) distributed across the rice genome. These lincRNAs produce 21-nt phasiRNA. The Argonaute MEL1binds to phasiRNA and regulates pollen mother cell development (Komiyaet al. 2014). The Osa-miR2118 triggered the sequence-specific cleavage of Pms1 that controls the photoperiod-sensitive male sterile gene PSMS in rice. Loss-of-function mutation in Pms1 affects the fertility by accumulation of Osa-miR2118 -cleaved phasiRNA under long day condition (Fan et al. 2016).
More recently, the Osa-miR2118 has also been shown to be involved in 21-nt phasiRNAs, which is responsible for anther wall development in rice (Araki et al. 2020). The miR482/2118 family was shown to affect disease resistance in tomato through the regulation of leucine- rich repeat proteins (Shivaprasad et al. 2012; Canto-Pastor et al. 2019). The phasiRNA that targets the conserve motifs of CC-NBS-LRR has been explored in diverse plant species, including spruce, grapevine, poplar, cotton, Arabidopsis  and citrus (Källman, Chen, Gyllenstrand & Lagercrantz 2013; Boccaraet al. 2014) suggesting that highly conserved siRNAs may be important in optimizing the expression of NBS-LRR genes, leading to compromised plant fitness. However, the precise role of phasiRNA in regulation of NBS-LRR immune receptors in rice is yet to be fully understood (Fei et al. 2013).