Molecular genetics of resistance to Spongospora subterranea f. sp. subterranea infection in potato (Solanum tuberosum L.)

Abstract

Infection of potato by Spongospora subterranea (Wallr.) Lagerh. f. sp. subterranea Tomlinson (Sss) causes tuber lesions, which directly affect the quality and marketability of the tubers, as well as root infections, which are associated with tuber yield and weight reductions. The pathogen is also a vector of potato mop-top virus (PMTV), which is considered economically important in some potato growing countries. Management of Sss is difficult because of the ineffectiveness of the current control options and it therefore requires integration of different control measures, of which host resistance represents the most economical, long-term approach. However, the information on the mechanisms of potato resistance to Sss infection is limited. In this study, the molecular and biochemical mechanisms of different potato cultivars that vary in their susceptibility to Sss infection were assessed. Potato cultivars commonly grown in South Africa were assessed for their differential responses to Sss root and tuber infection. A greenhouse pot trial was conducted to evaluate the susceptibility of 10 cultivars to Sss infection. Visual observation was performed to determine the severity of root galling and powdery scab infection, while root microscopic examination was carried out to assess root zoosporangia infection. Quantitative polymerase chain reaction (qPCR) was used to confirm and measure the quantity of Sss DNA in the inoculated and not-inoculated potato roots and tubers. No potato cultivar was found to be resistant to Sss root or tuber infection in this study, as all cultivars had zoosporangia and root galls on or in the roots, and powdery scab lesions on tubers, with the exception of cultivar Innovator, which did not show any powdery scab symptoms on progeny tubers. However, a range of susceptibility of potato cultivars to root infection, root gall formation and powdery scab, from tolerant to susceptible was observed in the study. There was no association between development of root diseases and powdery scab. A negative correlation was observed between powdery scab and number of root zoosporangia, with a weak positive correlation observed between powdery scab and number of root galls. Nevertheless, three cultivars; Fianna, Lanorma and Mondial were found to be moderately tolerant to all three diseases. These results were confirmed with qPCR, in which the amounts of Sss DNA confirmed the presence of Sss infection in roots and tubers of all 10 cultivars evaluated. The molecular mechanisms underlying quantitative potato resistance to powdery scab; discovery of defense-related genes was undertaken by ribonucleic acid sequencing (RNA-seq) in a susceptible and tolerant potato cultivar in response to powdery scab infection. Validation of the RNA-seq results and gene expression profile analysis of the two cultivars were carried out using quantitative real-time reverse transcriptase PCR (RT-qPCR) on a subset of genes induced at different tuber developmental stages. Differentially expressed genes related to plant defense responses were identified in both cultivars. Expression of nine genes involved in defense was up-regulated more in the tolerant cultivar than in the moderately susceptible cultivar upon infection by Sss. The involvement of defense-related metabolites in potato root tolerance to Sss root infection was investigated. Metabolic profiling of the chemicals in root exudates and root extracts of potato cultivars differing in susceptibility to Sss root infection, using a non-targeted metabolomics approach, was carried out. Ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) analysis was used to compare metabolic profiles of tolerant cultivars and susceptible cultivars inoculated or not-inoculated with Sss, to identify and quantify the resistance-related (RR) metabolites involved. Significant differences between the moderately tolerant (Fianna, Innovator, Lanorma, Mondial and Valor) and the moderately susceptible/susceptible (Avalanche, BP1, Ronaldo Sifra and Up-to-date) cultivar groups were identified in the levels of several metabolites, including amino acids, organic acids, alkaloids, phenolics and sugars. These secondary metabolite classes play important roles in plant defense. Monitoring Sss development in potato roots and tubers can enable efficient assessment of Sss infection in potatoes, resulting in proper, timely and improved control strategies for the diseases. Moreover, more information on the chemical composition of roots and root exudates as well as identification of defense-related genes is important for marker-assisted selection of potato germplasm in breeding programs for developing novel potato cultivars with broad and durable resistance to Sss.