Kartuli-lehemädaniku tekitaja Phytophthora infestans Baltikumi populatsioonide mitmekesisus

A Thesis for applying for the degree of Doctor of Philosophy in Agriculture.Late blight, caused by the oomycete Phytophthora infestans (Mont. de Bary 1876), is one of the most economically damaging plant diseases and certainly the most devastating disease in potato. The current research results of the Baltic P. infestans population are valuable and comparable with other populations on a larger scale because standardised genotyping methods were applied. The P. infestans populations of Estonia, Latvia, and Lithuania analysed with molecular SSR markers showed that frequent sexual recombination events have resulted in high genetic diversity, a large number of unique genotypes, and some local clones adapted to regional conditions. On the positive side, there was no evidence of invasive clonal lineages originating from other parts of Europe spreading or dominating in this region in the studied years. It would appear that local populations established from soilborne oospores early in the season are well adapted to the conditions in the Baltic countries. In the Estonian P. infestans population both mating types A1 and A2 were present at the majority of studied potato fields with nearly equal distribution of A1 and A2 isolates in the population. The evidence demonstrates that in the Baltic countries the introduction of a diverse population has established residential sexual populations in agricultural fields and the soil has become a source of inoculum. For sustainable potato production current disease management strategies should be adjusted according to the pathogen population status. Changes in pathogen populations directly affect the breeding and deployment of disease resistant cultivars, the performance of disease warning systems, and the efficacy of fungicides. Potato growers should be advised to implement late blight preventive measures, such as longer field rotation, to minimise oospore infections, and to use more disease resistant cultivars and high-quality seed potatoes. Timely fungicide treatments, using different active ingredients, in conventional fields are necessary to prevent foliage and tuber infection, stop late blight from spreading, and avoid resistance in pathogen populations.Tänu suurele geneetilisele mitmekesisusele on kartuli-lehemädanikku põhjustav munasseen Phytophthora infestans (Mont.) de Bary saavutanud hea kohastumisvõime erinevates klimaatilistes ja põllumajanduslikes ökosüsteemides, põhjustades laiaulatuslikke lehemädaniku epideemiaid. Kartuli-lehemädanikutekitaja P. infestans populatsiooniuuringud on vajalikud jälgimaks populatsioonides toimuvaid muutusi, et asjakohaste ennetus- ja tõrjevõtetega reageerida ja nõustada põllumajandustootjaid, sordiaretajaid ja konsulente. Käesolevas doktoritöös analüüsiti esmakordselt P. infestans Baltimaade populatsioonide struktuuri ja mitmekesisust SSR markerite abil. Käesoleva uurimistöö tulemused näitasid, et Eesti, Läti ja Leedu kartuli-lehemädaniku tekitaja P. infestans populatsioonid on sagedase sugulise paljunemise tulemusel geneetiliselt väga mitmekesised. Nendes populatsioonides esineb suur hulk unikaalseid genotüüpe, kuid leidub ka kohalikke kloone, mis on kohastunud piirkonnas paljunema, levima ja ellu jääma. Baltimaade P. infestans populatsioonides levinud genotüüpide ja geneetilise mitmekesisuse uurimine kasutades geneetilisi SSR markereid oli esmakordne. Teistes Euroopa riikides laialt levinud invasiivseid kloone Balti riikides veel ei tuvastatud, kuid arvestades patogeeni väga hea kohastumisvõime ja muutuvate kliimatingimustega, on see tõenäoline. P. infestans isolaatide paarumistüüpide A1 ja A2 esinemine Eestis on peaaegu võrdne ja paarumistüübid esinevad enamasti koos samadel põldudel, mis suurendavad sugulise paljunemise toimumise tõenäosust. Tulenevalt sugulise paljunemise võimekusest ja suurest geneetilisest mitmekesisusest Baltimaade P. infestans populatsioonides, tuleks kartulikasvatajatel lehemädaniku nakkusohu vähendamiseks hoida põldudel pikemat viljavaheldust (vähemalt 4 aastat), kasvatada lehemädanikule resistentsemaid sorte ja kasutada haigusvaba sertifitseeritud seemnekartulit. Kartulipõldude õigeaegne ja mõistlik töötlemine fungitsiididega, kasutades erineva toimeainega preparaate, on vajalik taimiku ja mugulate nakatumise vältimiseks, lehemädaniku leviku pidurdamiseks ja resistentsete patogeenipopulatsioonide tekke vältimiseks. Patogeeni genotüüpide ja kloonide levikut ning ellujäämist Balti riikides tuleb järjepidevalt jälgida, et populatsiooni muutustele asjakohaste ennetus- ja tõrjevõtetega reageerida.Publication of this thesis is supported by the Estonian University of Life Sciences

Physiological disorders affect apple susceptibility to Penicillium expansum infection and increase probability for mycotoxin patulin occurrence in apple juice

ArticlePenicillium expansum infection of apples and mycotoxin patulin (PAT) production has previously been associated with many pre- and postharvest factors other than physiological disorders. In the current study, ‘Antei’ and ‘Krameri tuviõun’ apples with and without bitter pit (BP) symptoms and ‘Talvenauding’ apples with and without superficial scald (SS) symptoms were used in order to determine if the named physiological disorders may influence susceptibility to P. expansum infection and PAT production. Apples were inoculated with 10 μL P. expansum spore suspension with the concentration of 1×105 conidia mL-1 and stored at 24 °C with relative humidity (RH) 80%. After 7 and 11 days, lesion diameters were measured, and apples were pressed into juice. PAT content was determined in pasteurized juice. Two cultivars out of three showed that in fruit with physiological disorders, Penicilllium infection and PAT production proceeded significantly faster compared to apples, which did not have physiological disorders. SS increased the risk for PAT occurrence in juice more than BP: while the juice pressed from BP–affected apples with no visual signs of fungal diseases did not contain PAT, juice pressed from apples with SS contained PAT three times above legislative limits defined by the World Health Organization (50 μg L-1)

Fungicide Resistance Evolving in Ramularia collo-cygni Population in Estonia

Ramularia leaf spot caused by the fungus Ramularia collo-cygni, has recently become widespread in Estonian barley fields. Currently, disease control in barley fields relies on SDHI and DMI fungicides, which might be threatened by R. collo-cygni isolates that are well-adapted to fungicide pressure. In a two-year study, 353 R. collo-cygni isolates were collected from spring barley fields in Estonia. A total of 153 R. collo-cygni isolates were examined for sensitivity to azoles (DMIs; prothioconazole-desthio, epoxiconazole, mefentrifluconazole) and succinate dehydrogenase inhibitors (SDHIs; boscalid, fluxapyroxad). Epoxiconazole was the least effective and a new fungicide mefentrifluconazole was the most effective DMI. Among SDHIs, fluxapyroxad was more effective than boscalid. Also, single R. collo-cygni isolates with high resistance to tested fungicides occurred, which could affect fungicide control of the pathogen. The entire collection of R. collo-cygni was analysed for mutations in fungicide target proteins. Six mutations were identified in CYP51 gene, the most dominant being I381T, I384T, and S459C. Also, numerous point mutations in the SdhC gene were present. The mutation G143A in strobilurin target protein CytB dominates in over 80% of the R. collo-cygni population, confirming the low efficacy of strobilurin fungicides in barley disease control

Challenges in Ramularia collo-cygni Control

Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, has recently become widespread in Europe. Succinate dehydrogenase inhibitor (SDHI) and demethylation inhibitor (DMI) fungicides are mainly applied for disease control on barley fields, but pathogen isolates with a reduced sensitivity can cause difficulties. There is an urgent need for new spring barley cultivars that are more resistant to RLS development and can inhibit R. collo-cygni epidemics

Changes in DMI, SDHI, and QoI Fungicide Sensitivity in the Estonian Zymoseptoria tritici Population between 2019 and 2020

Zymoseptoria tritici (Zt) populations adapt under the selection pressure of fungicides applied for disease control. The primary objective of this study was to assess fungicide sensitivity in the Estonian Zt population. A total of 282 Zt isolates from 2019 and 2020 were tested for sensitivity to azoles (DMIs; prothioconazole-desthio, epoxiconazole, mefentrifluconazole) and succinate dehydrogenase inhibitors (SDHIs; boscalid, fluxapyroxad). The efficacy of the tested fungicides varied considerably between the Estonian counties, but the Zt population is mainly sensitive to DMIs. Additionally, the frequencies of CYP51 gene alterations varied; D134G, V136C, A379G, and S524T had increased, but V136A and I381V showed a moderate decrease in 2020 in comparison to 2019. Sensitivity to SDHIs was stable, but boscalid was less effective than fluxapyroxad. SdhC gene mutations C-T33N, C-T34N, and C-N86S were common, but not linked with SDHI fungicide sensitivity assay results. Otherwise, mutation B-N225I in the SdhB subunit occurred in isolates with reduced sensitivity to SDHIs. Sensitivity to strobilurins was evaluated by the mutation G143A in the CytB gene, which was present in nearly half of the population. The data presented confirm the ongoing evolution of fungicide sensitivity in the Zt population in Estonia and highlight the importance of knowledge-based decisions for optimizing anti-resistance strategies in the field

High genotypic diversity found among population of Phytophthora infestans collected in Estonia

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Examining Phenotypic Traits Contributing to the Spread in Northern European Potato Crops of EU_41_A2, a New Clonal Lineage of Phytophthora infestans

International audienceUntil recently, genotypes of Phytophthora infestans were regionally distributed in Europe, with populations in western Europe being dominated by clonal lineages and those in northern Europe being genetically diverse because of frequent sexual reproduction. However, since 2013 a new clonal lineage (EU_41_A2) has successfully established itself and expanded in the sexually recombining P. infestans populations of northern Europe. The objective of this study was to study phenotypic traits of the new clonal lineage of P. infestans, which may explain its successful establishment and expansion within sexually recombining populations. Fungicide sensitivity, aggressiveness, and virulence profiles of isolates of EU_41_A2 were analyzed and compared with those of the local sexual populations from Denmark, Norway, and Estonia. None of the phenotypic data obtained from the isolates collected from Denmark, Estonia, and Norway independently explained the invasive success of EU_41_A2 within sexual Nordic populations. Therefore, we hypothesize that the expansion of this new genotype could result from a combination of fitness traits and more favorable environmental conditions that have emerged in response to climate change

Investigating phenotypic traits as potential drivers of the emergence of EU_37_A2, an invasive new lineage of Phytophthora infestans in Western Europe

International audienceSince the mid-2010s, Phytophthora infestans clones that have been dominant in Western Europe from the beginning of the 21st century, for example, EU_13_A2, EU_6_A1 and EU_1_A1, are being replaced by several other emerging clones, including EU_37_A2. The objective of this study was to determine whether the main drivers for the success of EU_37_A2 in Western Europe are associated with decreased fungicide sensitivity, increased virulence and/or aggressiveness. Axenic P. infestans cultures were sampled in the 2016 and 2017 growing seasons from potato crops in France and the United Kingdom. Amongst these, four genotypes were identified: EU_37_A2, EU_13_A2, EU_1_A1 and EU_6_A1. Although a wide range of fluazinam sensitivity was found amongst individual isolates, clonal lines EU_13_A2 and EU_37_A2 showed decreased sensitivity to fluazinam. EU_37_A2 overcame the R5 differential cultivar more often than isolates of EU_1_A1 or EU_6_A1. However, this does not explain the competitive advantage of EU_37_A2 over the virulent EU_13_A2. The fittest genotype, as measured by aggressiveness under controlled conditions, was EU_6_A1, followed by EU_37_A2, EU_13_A2 and then EU_1_A1. EU_37_A2 isolates also showed a shorter latent period than either EU_6_A1 or EU_13_A2, which could favour its long-term persistence. Overall, the data suggest that the emergence of EU_37_A2 in Western Europe was driven by its resistance to a then-major fungicide and shorter generation time. This conclusion is further supported by the fact that EU_37_A2 emergence was slowed by the progressive reduction in the use of fluazinam as a single active ingredient in the years following its initial detection