A role for small RNA in regulating innate immunity during plant growth

<div><p>Plant genomes encode large numbers of nucleotide-binding (NB) leucine-rich repeat (LRR) immune receptors (<i>NLR</i>) that mediate effector triggered immunity (ETI) and play key roles in protecting crops from diseases caused by devastating pathogens. Fitness costs are associated with plant <i>NLR</i> genes and regulation of <i>NLR</i> genes by micro(mi)RNAs and phased small interfering RNAs (phasiRNA) is proposed as a mechanism for reducing these fitness costs. However, whether <i>NLR</i> expression and <i>NLR</i>-mediated immunity are regulated during plant growth is unclear. We conducted genome-wide transcriptome analysis and showed that <i>NLR</i> expression gradually increased while expression of their regulatory small RNAs (sRNA) gradually decreased as plants matured, indicating that sRNAs could play a role in regulating <i>NLR</i> expression during plant growth. We further tested the role of miRNA in the growth regulation of <i>NLRs</i> using the tobacco mosaic virus (TMV) resistance gene <i>N</i>, which was targeted by miR6019 and miR6020. We showed that <i>N</i>-mediated resistance to TMV effectively restricted this virus to the infected leaves of 6-week old plants, whereas TMV infection was lethal in 1- and 3-week old seedlings due to virus-induced systemic necrosis. We further found that <i>N</i> transcript levels gradually increased while miR6019 levels gradually decreased during seedling maturation that occurs in the weeks after germination. Analyses of reporter genes in transgenic plants showed that growth regulation of <i>N</i> expression was post-transcriptionally mediated by <i>MIR6019/6020</i> whereas <i>MIR6019/6020</i> was regulated at the transcriptional level during plant growth. TMV infection of <i>MIR6019/6020</i> transgenic plants indicated a key role for miR6019-triggered phasiRNA production for regulation of <i>N</i>-mediated immunity. Together our results demonstrate a mechanistic role for miRNAs in regulating innate immunity during plant growth.</p>