Genetic profiling of potato resistances to Globodera pallida

Potato is the third most important food crop globally. However, Potato Cyst Nematodes (PCN) pose a significant threat to sustainable crop production as a major soil-borne pest. Effective control of PCN can be achieved through the use of disease resistance genes, particularly those belonging to the nucleotide-binding, leucine-rich-repeat (NLR) gene family. The two primary aims of this thesis are: (1) to develop a robust, widely applicable, and cost-effective process for identifying NLR genes, and (2) to identify candidate NLRs associated with resistance to Globodera pallida (pathotypes Pa2/3), including Gpa5, Gpa6, and Grp1. Ultimately, this work seeks to explain the phenotypic variation in resistance to G. pallida among potato varieties based on the combined effect of these three genes, providing a genetic foundation for resistance breeding. I successfully implemented SMRT-AgRenSeq in tetraploid potatoes to identify functional NLR genes. Additionally, I integrated dRenSeq into the methodology, using an F1 score to express the strength of linkage for candidate filtering. This comprehensive approach is termed SMRT-AgRenSeq-d. Through SMRT-AgRenSeq-d analyses, four benchmark resistance genes—Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b—were reliably identified in a panel of 117 varieties exhibiting varying phenotypic penetrations. All benchmark genes were identified with an F1 score of 1, indicating absolute linkage within the panel. SMRT-AgRenSeq-d was further applied to investigate the elusive nematode resistance genes Gpa5, Gpa6, and Grp1. For Gpa5, nine strong candidate genes were identified with the same panel, and they were mapped to the previously established location on potato chromosome 5. These candidates are potential homologs of the late blight resistance gene R1. After further filtering using RNA-Seq data, seven candidates remained, which were subsequently subjected to RNAi silencing experiments which are still ongoing. Additionally, a new kind of haplotype-based marker was developed for Gpa5. Furthermore, SMRT-AgRenSeq-d identified 34 NLR candidates for Gpa6, with six being the most likely candidates, and three candidates for Grp1. In total, 88.4% of the observed G. pallida resistance in potato cultivars and breeding clones could be explained by the distribution of the Gpa5, Gpa6, and Grp1 genes.