Phytophthora infestans is the causal agent of late blight in potato. The occurrence of P. infestans with both A1 and A2 mating types in the field may result in sexual reproduction and the generation of recombinant strains. Such strains with new combinations of traits can be highly aggressive, resistant to fungicides, and can make the disease difficult to control in the field. Metalaxyl-resistant isolates are now more prevalent in potato fields. Understanding the genetic structure and rapid identification of mating types and metalaxyl response of P. infestans in the field is a prerequisite for effective late blight disease monitoring and management. Molecular and phenotypic assays involving molecular and phenotypic markers such as mating types and metalaxyl response are typically conducted separately in the studies of the genotypic and phenotypic diversity of P. infestans. As a result, there is a pressing need to reduce the experimental workload and more efficiently assess the aggressiveness of different strains. We think that employing genetic markers to not only estimate genotypic diversity but also to identify the mating type and fungicide response using machine learning techniques can guide and speed up the decision-making process in late blight disease management, especially when the mating type and metalaxyl resistance data are not available. This technique can also be applied to determine these phenotypic traits for dead isolates. In this study, over 600 P. infestans isolates from different populations—Estonia, Pskov region, and Poland—were classified for mating types and metalaxyl response using machine learning techniques based on simple sequence repeat (SSR) markers. For both traits, random forest and the support vector machine demonstrated good accuracy of over 70%, compared to the decision tree and artificial neural network models whose accuracy was lower. There were also associations (p < 0.05) between the traits and some of the alleles detected, but machine learning prediction techniques based on multilocus SSR genotypes offered better prediction accuracy.

There is limited understanding of the genetic variability in Phytophthora infestans in the major potato cultivation region of north-western Russia, where potato is grown primarily by small households with limited chemical treatment of late blight. In this study, the mating type, sensitivity to metalaxyl, and genotype and population genetic diversity (based on 12 simple sequence repeat (SSR) markers) of 238 isolates of P. infestans from the Pskov region during the years 2010–2013 were characterized. The aim was to examine the population structure, phenotypic and genotypic diversity, and the prevalent reproductive mode of P. infestans, as well as the influence of the location, time, and agricultural management practices on the pathogen population. The frequency of the A2 mating was stable over the four seasons and ranged from 33 to 48% of the sampled population. Both mating types occurred simultaneously in 90% of studied fields, suggesting the presence of sexual reproduction and oospore production in P. infestans in the Pskov region. Metalaxyl-sensitive isolates prevailed in all four years (72%), however, significantly fewer sensitive isolates were found in samples from large-scale conventional fields. A total of 50 alleles were detected in the 141 P. infestans isolates analyzed for genetic diversity. Amongst the 83 SSR multilocus genotypes (MLGs) detected, 65% were unique and the number of MLGs varied between locations from 3 to 20. These results, together with the high genotypic diversity observed in all the locations and the lack of significance of linkage disequilibrium, suggest that sexual recombination is likely responsible for the unique MLGs and the high genetic diversity found in the Pskov region population, resembling those of north-eastern European populations.

The soil fungal community plays an important role in determining plant growth and health. In this study, we investigated the fungal diversity and community composition in the roots and soil of 21 potato (Solanum tuberosum L.) cultivars using high-throughput sequencing at three different time points across the growing season. In soil and roots, the fungal richness and relative abundance of pathogens and saprotrophs were mainly affected by sampling time. While sampling time affected fungal composition in soil, root fungal communities were also significantly affected by cultivar. The cultivar had the strongest effect on diversity of pathogens and abundance of particular pathogen species. Our results demonstrate changes in soil and root fungal communities of potato over the growing season, as well as highlighting the importance of potato cultivar on root fungal communities and abundance of pathogens.

The aim of this study was to evaluate foliar late blight resistance and yield of selected foreign and Estonian potato cultivars, to determine the most promising cultivars for the northern Baltic region. We hypothesized that local cultivars have higher potato late blight (Phytophthora infestans) resistance and yield due to higher blight resistance. Potato late blight observation field trials were carried out in 2012 and 2013 in Einola Farm, Tartu County, Estonia. In both growing seasons, twelve potato cultivars were compared: nine from the Dutch breeding company "Agrico" and three from the Estonian Crop Research Institute (ECRI). They comprised four early cultivars 'Ranomi', `Esmee', 'Romie' and `Maree, four medium early cultivars 'Toluca', 'Mariska', 'Madeleine' and 'Teele', and four medium late / late cultivars 'Excellency', 'Bellefleur', `Manitou' and 'Anti'. Of these, only two, 'Anti' and 'Toluca', qualified as highly foliar late blight resistant. This research clearly indicates that, despite unfavourable conditions for the pathogen, late blight is able to destroy potato foliage in most of these cultivars before the end of the growing season in northern Baltic conditions. This reflects local genetic heterogeneity of populations of P. infestans, probably associated with the presence of strains adapted to a wide range of humidity conditions. In 2012 that had late blight favourable weather, the cultivar 'Toluca' showed high foliar blight resistance, as it reached the maximum yield compared to other cultivars, which were susceptible or very susceptible to late blight and had drastically reduced yield. However, although the late blight infection was not recorded in the growing season 2013, the cultivar 'Toluca' did not tolerate the dry weather well and its tuber yield remained significantly lower than that in all other cultivars. Additionally, in 2013, a potato early blight (Alternaria solani) outbreak was recorded with the two most susceptible cultivars being the local cultivar 'Teele' and the Dutch cultivar 'Excellency'.