CsRDR1b and CsRDR1c genes in Cucumis sativus are crucial for plant defense against virus and oomycete co-infection

Cucumber harbors RNA-dependent RNA polymerase 1 (RDR1) gene family of four genes (CsRDR1a, CsRDR1b, and CsRDR1c1/c2), which are induced upon virus infection. This study examined the roles of cucumber RDR1b and RDR1c1/c2 in defense against cucumber green mottle mosaic virus (CGMMV) during single and mixed infection with Pythium spp. Co-infection with CGMMV and the necrotrophic pathogen Pythium spinosum (P. spinosum) leads to the extensive synergetic collapse, which resulted in 45–50% mortality of csrdr1c mutants and 20–31% mortality of csrdr1b mutants by 11 dpi at 32 °C, compared to 100% survival of wild-type (WT) vs. Ilan cucumber plants; similar patterns were observed at 25 °C. At 17 dpi, the csrdr1c mutants reached 100% mortality compared to 100% survival of WT. In the experimental infection system in commercial greenhouses, when both pathogens can be preserved in soil from the previous growing cycle, the mortality rates reached 67–75% and 28–37% in csrdr1c and csrdr1b mutants, respectively, while WT plants remained unaffected 30 days post-planting. Leaf samples were subjected to high-throughput sequencing (HTS), followed by bioinformatics and KEGG pathway analysis demonstrated that the major differences in gene expression were associated with downregulation. Phenylpropanoid biosynthesis was the most significantly downregulated pathway with 15 downregulated genes in csrdr1c and csrdr1b mutants. Expression of key genes such as phenylalanine ammonia-lyase (PAL) and peroxidases was suppressed by 2- to 8-fold in non-infected CGMMV and P. spinosum csrdr1c and csrdr1b mutants, indicating a consequent reduction in phenylpropanoid biosynthesis. Following CGMMV infection and mixed infection of CGMMV with P. spinosum, KEGG analysis demonstrated no major differences in gene expression at the foliar parts. Our results demonstrate the interaction between CsRDR1, PAL, and peroxidase in plant pathogen defense, and the suppression of these enzymes was associated hypersensitivity of csrdr1 mutants to co-infection.