Effectoromics screening identifies non-canonical TN genes in pepper contributing to Phytophthora capsici resistance

Abstract Text: Pepper (Capsicum spp.) is a globally important crop; however, its production is severely threatened by Phytophthora blight caused by Phytophthora capsici. Although the Mexican landrace CM334 is a well-utilized resistant resource, the specific genes conferring immunity to P. capsici remain unidentified. Here, by integrating receptoromics and effectoromics, we established a high-throughput co-expression screening platform in N. benthamiana to dissect the ETI interaction network between pepper landrace CM334 and P. capsici LT1534. Screening of 430 RXLR P. capsici effectors and 426 pepper NLRs in N. benthamiana revealed a diverse repertoire of ETI mediated by NLR-AVR interactions, leading to the identification of three non-canonical TN genes that confer resistance to P. capsici. Further analysis showed these TN genes form a tandemly arrayed cluster alongside a full-length TNL with high sequence similarity. Functional assays demonstrated that only the truncated TN genes are specifically activated by the effector PC160, triggering a hypersensitive response (HR) in N. benthamiana in an NRG1- and EDS1-dependent manner. Comparative synteny analysis revealed that truncated TN genes are present only in the resistant CM334 genome but absent in susceptible varieties. These findings provide a framework for rapid identification of novel resistance genes independent of genetic populations and offer valuable genetic resources and theoretical foundations for breeding disease-resistant crops.