Soybean RNA polymerases IV and V repress defense response genes and plant immunity

Transposon silencing via RNA-directed DNA methylation (RdDM) is mediated primarily through 24-nucleotide (nt) small-interfering RNAs (siRNAs) and 2 plant-specific RNA polymerases, Pol IV and Pol V. We generated and characterized RNA-interference (RNAi) lines targeting the largest subunit of Pol IV and Pol V and the second-largest subunit shared by Pol IV and Pol V in soybean. Our analyses showed that the canonical roles of Pol IV and Pol V in RdDM as described in Arabidopsis, whereby Pol IV produces 24-nt siRNAs and Pol V recruits siRNAs to homologous loci to trigger DNA methylation, are conserved in soybean. Our analyses also uncovered previously unknown functions of Pol IV and Pol V in that they repress defense response genes en masse. These genes normally undergo RdDM and are silenced, but they are de-repressed when Pol IV and Pol V are knocked down. Furthermore, the de-repression of a set of defense-related genes channeled their RNAs into the RNAi pathway to produce 21- to 22-nt siRNAs. Knocking down Pol IV and Pol V either singly or together led to increased resistance against the oomycete pathogen Phytophthora sojae, suggesting that Pol IV- and Pol V-mediated gene silencing regulates plant immunity.