Identification and Expression Analyses of Atypical NLR Genes in Potato

Defense responses against pathogens are essential for plant growth, and the nucleotide-binding leucine-rich repeat receptor (NLR) family is an important component of plant immunity. Besides NBS and LRR domains, NLR proteins also contain TIR, CC, or RPW8 domain at their N-terminus and the functions of these canonical domains are well documented. Recently, some atypical X domains, also named integrated domains (IDs), have been reported to be encoded by NLR genes and to play key roles in effector-triggered immunity. Here, we screened the plant NLR database to identify atypical NLRs in potato. A total of 181 atypical NLR protein entries, identified from 642 candidates as truncated or St-NLR-IDs (potato NLRs encoding ID) and comprising 147 NLR-IDs and 34 truncated NLRs, were classified into four major groups, including T(TIR)-class, C(CC)-class, N(NBS)-class, and X-class, and together with 12 typical CNL/TNL sequences, they were used for phylogenetic analysis. Promoter regions of the majority of these entries contain “stress and defense” elements such as MYB/MYC cis-regulatory element, indicating their involvement in plant immune response. In the Rywal background, the expression of six genes was upregulated and that of nineteen genes was downregulated. In the NahG-Rywal plants, the expression of seventeen genes was upregulated and that of eight genes was downregulated. In the shRBOHD-Rywal background, the expression of eighteen genes was upregulated and that of six genes was downregulated. We also investigated the expression of four C-JID-containing NLR-ID genes, M1BEE2, M1BF53, M1A5Z0, and M1BZB1, upon PVX, PVY infection and SA treatment by RT-qPCR and suggested their potential involvement in plant immunity. Promoter–GUS assays for the above four genes also supported their responses to viral infection and SA treatment. In summary, we identified and classified atypical NLRs in potato, analyzed their expression under PVYN-Wilga infection using public transcriptome data, and validated the virus- and SA-responsive expression of four C-JID-encoding genes, providing a resource for future functional studies.