Keep up your guard: basal expression of defence mechanisms distinguishes blight resistant from blight susceptible potato varieties

Abstract Background A key goal in potato breeding is to develop potato varieties with more durable quantitative resistance to late blight, enabling disease to be managed while reducing pesticide inputs. This study aimed to identify key features associated with resistance to late blight to facilitate the development of more resistant potato cultivars, including candidate genes and their expression patterns before and in response to pathogen inoculation. Results Comparative transcriptomic analysis of leaf tissue in two resistant Sarpo varieties and one susceptible variety (Duke of York) revealed widespread differences in gene expression both before and during infection with P. infestans . In response to infection, many more genes were downregulated in Duke of York than in the resistant varieties, including genes involved in ABA and jasmonic acid hormone signalling pathways and signal transduction through phosphorylation. In all three varieties, genes involved in lignin biosynthesis were upregulated in response to infection, though the resistant varieties responded more strongly and already expressed lignin-related genes at a higher level in healthy uninfected leaves. Across many functional categories, stressed-like expression patterns in healthy leaves before the onset of stress that persist during infection may contribute to a more effective response to P. infestans in the resistant Sarpo varieties. These include consistent upregulation of beta-1,3-glucanases involved in degrading the pathogen cell wall, numerous specific resistance (R) genes, and wall-associated kinase (WAK) receptors that recognise pectin fragments from the cell wall during early stages of infection. Together with upregulation of specific pectin lyases, and a broad set of genes involved in protein phosphorylation, these differences may enable the Sarpo varieties to more rapidly induce both pattern triggered and effector triggered immunity, leading to higher resistance. Conclusions These findings paint a transcriptome-wide picture of the molecular basis of quantitative resistance to late blight and thus provide relevant insights that can help future efforts to breed blight resistant potato varieties.