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Primers/probes used for monitoring pathogen colonization

Primers/probes used for monitoring pathogen colonization

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The difficulty in subculturing biotrophic fungi complicates etiological studies related to the associated plant diseases. By employing internal transcribed spacer rDNA-targeted quantitative real-time polymerase chain reaction, we now show that the heteroecious rust Thekopsora areolata, commonly associated in natural conditions to sapling shoots and...

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... addition, we monitored the presence of G. abietina and Phomopsis sp., pathogenic fungi commonly associated with necrotic stem lesions in Norway spruce seedlings, with primer/ probe sets described by Børja et al. (3). The primer/probe sets used are shown in Table 2. ...

Citations

... without host alternation, usually appearing as uredinia, may also occur on Chamaenerion spp. (Gäumann 1941;Hietala et al. 2008). ...
... On the other hand, some previous authors, such as Kuprevich and Ul'yanishchev (1975), already recognized two species, in the latter case as P. abietischamaenerii and P. pustulata. However, taking into account the latest phylogenetic results for the P. epilobii complex (Hietala et al. 2008, the present work), connected with the phylogenetic differentiation of Epilobium s. lat. into two well-supported clades (Epilobium s. str. ...
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Using molecular phylogenetic analyses (ITS) and morphological data obtained from light and electron microscopy, some European and North American species and genera placed or formerly placed in the genus Pucciniastrum in the Coleosporiaceae and Pucciniastraceae (Pucciniales) were taxonomically revised. The ITS analyses confirmed recent familiar concepts based on less variable markers except for the genus Hyalopsora. The family Pucciniastraceae is characterized by Abietoideae (Abies, Tsuga) aecial hosts. Pucciniastrum is described as a genus that consists of host-alternating species forming aecia on needles of Abies hosts, with special features of aeciospore morphology, and Onagraceae telial hosts. Other genera in the Pucciniastraceae are Calyptospora, Melampsorella, and additional taxa, which are currently provisionally placed in Pucciniastrum, but must be revised in future studies. Pucciniastrum epilobii (s. lat.), the type species of Pucciniastraceae, represents at least two species with different life cycles and urediniospore characteristics and is lecto-and epitypified. The family Coleosporiaceae, characterized by Pinoideae (Pinus) and Piceoideae (Picea) aecial hosts, contains Rosaceae rusts from three well-supported clades represented by three genera, Thekopsora, Quasipucciniastrum, and Aculeastrum gen. nov. Aculeastrum is characterized by coarsely arcuate ostiolar peridial cells and infects Rubus spp. telial hosts. The following new taxonomic combinations are proposed: Calyptospora ornamentalis comb. nov., Quasipucciniastrum ochraceum comb. nov., Q. potentillae comb. nov, Aculeastrum americanum comb. nov., and A. arcticum comb. nov. The results are discussed with emphasis on future studies in Pucciniastrum and the P. epilobii complex and on nomenclatural changes necessary for rust fungi due to the Shenzhen Code.
... Pine twisting rust (Melampsora pinitorqua) occurs sporadically on Scots pine and maritime pine (Pinus pinaster) seedlings (Desprez-Loustau and Wagner, 1997; Kurkela and Lilja, 1984) but P. contorta seems to be resistant (Martinsson, 1985). Cherry spruce rust (Thekopsora areolata) may infect spruce seedlings (Hietala et al., 2008). Both rust species are spread by basidiospores in early summer when new succulent shoot tissues are susceptible to infection, which leads to twisting and canker formation of shoots ( Fig. 17.8) (Desprez-Loustau and Wagner, 1997;Hietala et al., 2008). ...
... Cherry spruce rust (Thekopsora areolata) may infect spruce seedlings (Hietala et al., 2008). Both rust species are spread by basidiospores in early summer when new succulent shoot tissues are susceptible to infection, which leads to twisting and canker formation of shoots ( Fig. 17.8) (Desprez-Loustau and Wagner, 1997;Hietala et al., 2008). Rust infections are often accompanied with other fungal species, and in nurseries Phomopsis sp. ...
... Rust infections are often accompanied with other fungal species, and in nurseries Phomopsis sp. (Hietala et al., 2008) and B. cinerea in young pine plantations (Domanski and Kowalski, 1988) have been reported in connection with rust infections. ...
Chapter
This chapter gives an overview on the current techniques of forest tree seedling production and reviews the effects of mycobiome on tree seedling condition. Firstly, the main fungal species causing diseases in forest nursery are discussed. The current state of knowledge of the rhizosphere and phyllosphere mycobiome of tree nursery species and their role as seedling endophytes or saprotrophs is presented. Special emphasis on the role of mycorrhizas in nursery environment and after planting is further highlighted. Finally, some integrated pest management (IPM) methods to suppress disease outbreaks in nurseries are briefly described. In addition, the impacts of the use of chemicals (e.g. fungicides) in plant protection in nurseries on the seedling mycobiome are discussed.
... Total DNA from the leaf spots was extracted with NucleoSpin Soil DNA extraction kit (Macherey-Nagel, Germany) according to the manufacturer's manual. The amount of T. areolata DNA in each sample was quantified by quantitative polymerase chain reaction (qPCR) with specific primers targeting an 81 bp sequence of the internal transcribed spacer (ITS) region (Hietala et al. 2008). To prepare standard samples, the 81 bp sequence was amplified using T. areolata genomic DNA and the same primers. ...
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The cherry spruce rust caused by Thekopsora areolata (Fr.) Magnus results in significant losses in spruce seed production in the forest industry. The pathogen is present in Asia and Europe but absent from North America where it has been considered as a potential threat and listed as a quarantine organism by the United States Department of Agriculture. A comprehensive list and in-depth information regarding the alternate hosts of this pathogen are important for conducting epidemiological studies and for optimal disease control. Prunus padus L. is the main alternate host reported for T. areolata. In this study, we investigated the susceptibility of domestic and exotic Prunus spp. and other potential alternate host-plant species native to Scandinavia to T. areolata infection through a field survey and aeciospore inoculation experiments in the greenhouse and laboratory. No new susceptible species were found. In Sweden, a new record of Prunus grayana Maxim. with low susceptibility to T. areolata was found. In addition, we updated the list of currently confirmed alternate hosts of T. areolata according to field observations and inoculation results. Prunus padus and Prunus serotina Ehrh., as well as their hybrids and subspecies of Prunus padus, are highly susceptible, while Prunus depressa Pursh, Prunus grayana, Prunus spinosa L., and Prunus tenella Batsch are considered slightly susceptible.
... Control of T. areolata is currently difficult, because the mode of spreading of the rust is poorly understood. The rust infects also Picea shoots, where it may sporulate (Roll-Hansen 1947) or occur as a latent pathogen (Hietala et al. 2008). It is unclear, if the disease control should be focused on alternate host eradication, cutting aecial sporulation on Picea, reducing insect incidence in cones or protection of cone infection by fungisides or bioproducts. ...
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The alternate host range of cherry-spruce rust is poorly studied although such information could be important in protecting spruce seed orchards from infections. Pathogenicity of cherry-spruce rust, (Fr.) Magnus, was investigated on potential alternate host species in a greenhouse and in a laboratory in Finland. Five common species of Ericaceae, L., L., L., L. and (L.) Spreng, were inoculated in the greenhouse using aeciospores from seven Norway spruce [ (L.) H. Karst.] seed orchards suffering from in 2018. In addition, young detached leaves of spp. and 17 other plant species of ground vegetation from eight Norway spruce seed orchards were inoculated with aeciospores from six seed orchards in the laboratory in 2019. Also, young leaves of L. trees growing within the seed orchards or close to them were inoculated as controls. None of the inoculated leaves of the potential alternate hosts formed uredinia either in the greenhouse or in the laboratory. In contrast, leaves of from the seed orchards were infected by the six spore sources from six seed orchards and produced uredinia. As spores were able to infect only , but not the other tested species belonging to ground flora, it was concluded that disperses only via spp. in Finnish seed orchards. Thekopsora areolata Vaccinium myrtillus V. uliginosum V. vitis-idaea Empetrum nigrum Arctostaphylos uva-ursi Picea abies T. areolata Vaccinium Prunus padus P. padus T. areolata P. padus T. areolata Prunus
... In addition to the cones of P. abies, the rust sporulates also on other spruce species, such as P. engelmannii Parry ex Engelm., P. glauca (Moench) Voss and P. omorika (Panĉić) Purk. that are non-native in Finland (Kaitera et al. 2009(Kaitera et al. , 2017 as well as in shoots of P. abies and P. engelmannii (Roll-Hansen 1947;Hietala et al. 2008). ...
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Thekopsora areolata Picea abies Picea T. areolata T. areolata Vaccinium myrtillus V. vitis-idaea Empetrum nigrum Calluna vulgaris Thekopsora areolata Thekopsora ² T. areolata V. myrtillus V. vitis-idaea V. myrtillus V. vitis-idaea V. myrtillus V. vitis-idaea Naohidemyces vaccinii Vaccinium T. areolata Prunus
... comm.) and the biological mechanisms how aeciospores could colonize cones are unknown. However, there is evidence of colonization of Picea shoots by T. areolata as reported by Hietala, Solheim, and Fossdal (2008) who found the fungus in 100 symptomatic young seedlings of P. abies by quantitative PCR (Hietala et al., 2008). Among other rusts, the autoecious stem rust on Scots pine, P. pini, is able to infect the host by aeciospores, grow and sporulate from spermogonia and aecia in host tissues systematically for years (Kaitera & Nuorteva, 2008). ...
... comm.) and the biological mechanisms how aeciospores could colonize cones are unknown. However, there is evidence of colonization of Picea shoots by T. areolata as reported by Hietala, Solheim, and Fossdal (2008) who found the fungus in 100 symptomatic young seedlings of P. abies by quantitative PCR (Hietala et al., 2008). Among other rusts, the autoecious stem rust on Scots pine, P. pini, is able to infect the host by aeciospores, grow and sporulate from spermogonia and aecia in host tissues systematically for years (Kaitera & Nuorteva, 2008). ...
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Rust fungi are obligate parasites, of plants, with complex and in many cases poorly known life cycles which may include host alteration and up to five spore types with haploid, diploid, and dikaryotic nuclear stages. This study supports that Thekopasora areolata , the causal agent of cherry‐spruce rust in Norway spruce, is a macrocyclic heteroecious fungus with all five spore stages which uses two host plants Prunus padus and Picea abies to complete its life cycle. High genotypic diversity without population structure was found, which suggests predominantly sexual reproduction, random mating and a high gene flow within and between the populations in Fennoscandia. There was no evidence for an autoecious life cycle resulting from aeciospore infection of pistillate cones that would explain the previously reported rust epidemics without the alternate host. However, within cones and scales identical multilocus genotypes were repeatedly sampled which can be explained by vegetative growth of the fertilized mycelia or repeated mating of mycelium by spermatia of the same genotype. The high genotypic diversity within cones and haplotype inference show that each pistillate cone is infected by several basidiospores. This study provides genetic evidence for high gene flow, sexual reproduction, and multiple infections of Norway spruce cone by the rust fungus T. areolata which expands the general understanding of the biology of rust fungi.
... Moreover, P. padus is susceptible to bacterial cankers caused by Xanthomonas arboricola pv pruni, and Pseudomonas syringae [14,63,64]. Further, Prunus padus is a host of cone rust in Norway spruce caused by the rust fungi Thekopsora areolata, that also can kill the top shoots of Norway spruce, and is heteroecious with Chrysomyxa pirolata that forms spermatogonia (undifferentiated male germ cells) [65,66]. Also, viruses like Prune dwarf virus and Prunus necrotic ring spot virus may be a problem in P. padus [67]. ...
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Prunus padus L. (bird cherry) belongs to the Racemosa group in subgenus Padus in the genus Prunus L. It is a hardy invasive species, which makes it valuable for securing slopes, and for eco-design. It is a good solitary park tree with early flowering of white flowers in racemes, which have a pleasant smell. However, it may be attacked by cherry-oat aphid, and the small ermine moth, which may weave giant webs over the whole tree, which demonstrates the important role of P. padus in the food web of forest ecosystems. The species is in balance with these pests, other herbivores and diseases throughout Europe and Asia. Another threat is the competition against the invasive P. serotina, but it seems that P. padus is not strongly threatened, though they compete for the same habitats. Moreover, human interference of forest community ecology is probably the greatest threat. The tree is not only winter hardy; it can also survive hot summers and tolerate a wide variety of soil types. It may form dense thickets due to the regeneration of branches bent to the ground and basal shoots, and may be invasive. These characteristics are important in determining the ecological niche of P. padus, which involves the position of the species within an ecosystem, comprising both its habitat requirements and the functional role. It is also important that P. padus has effective dispersal of pollen and seeds. This, together with the previously noted characteristics and the fact that the tree can cope well with climate change, define it as a not threatened species. However, the ssp. borealis is threatened and national level monitoring is required. Prunus padus has been exploited by farmers and rural population, but is less used today. However, it is still used for making syrup, jam and liquor. Moreover, the wood is valuable for wood carving and making cabinets. All tissues are valuable as sources of powerful natural antioxidants. However, the interest in the P. padus fruit and other tissues is overshadowed by the interest in other wild species of edible and human health-related berries. Moreover, the tree is used in horticulture as an ornamental in gardens and parks, values that deserve a new focus.
... The gene model shows an expression pattern strongly associated with differentiating and lignifying tissues in the P. abies exAtlas, particularly with young female cones. Clearly the candidate gene is active in tissues susceptible to the pathogen, and basidiospores of T. areolata are thought to infect Norway spruce cones and young shoots in the spring (Hietala, Solheim, & Fossdal, 2007;Kuporevich & Transhel, 1957). Thus, it is not far-fetched to imagine that MA_10g0010 may be associated with processes in these tissues that control their vulnerability to colonization, possibly through cell-wall enforcement (Elfstrand et al., 2001;Fagerstedt, Kukkola, Koistinen, Takahashi, & Marjamaa, 2010;Kärkönen, Warinowski, Teeri, Simola, & Fry, 2009;Marjamaa et al., 2006) or processes controlling the timing of bud break and bud flush; overexpression of the class III peroxidase SPI2 in Norway spruce plants led to significant delays of these process compared to in wild-type Norway spruce plants (Clapham, Häggman, Elfstrand, Aronen, & Arnold, 2003;Elfstrand et al., 2001). ...
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The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies (L.) H. Karst.) vegetative buds harbours active fungal communities but these are hitherto largely uncharacterized. This study combines ITS‐sequencing of the fungal communities associated with dormant vegetative buds with genome‐wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e. top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
... The genera included Puccinia (GenBank) Pucciniastrum, Uredinopsis, Cronartium (GenBank) and Melampsoridium as outgroup. GenBank accessions of Cronartium ribicola ITS sequences are DQ445908 (Hietala et al. 2008), GU727730 (Mulvey and Hansen 2011) and KX574673 (Vogler et al. 2017). GenBank accessions for Puccinia graminis are AY874141, AY874143 and AY874146 (Abbasi et al. 2005). ...
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Species of rust fungi of the genus Milesina (Pucciniastraceae, Pucciniales) are distributed mainly in northern temperate regions. They host-alternate between needles of fir ( Abies spp.) and fronds of ferns (species of Polypodiales). Milesina species are distinguished based on host taxonomy and urediniospore morphology. In this study, 12 species of Milesina from Europe were revised. Specimens were examined by light and scanning electron microscopy for urediniospore morphology with a focus on visualising germ pores (number, size and position) and echinulation. In addition, barcode loci (ITS, nad6, 28S) were used for species delimitation and for molecular phylogenetic analyses. Barcodes of 72 Milesina specimens were provided, including 11 of the 12 species. Whereas urediniospore morphology features were sufficient to distinguish all 12 Milesina species except for 2 ( M.blechni and M.kriegeriana ), ITS sequences separated only 4 of 11 species. Sequencing with 28S and nad6 did not improve species resolution. Phylogenetic analysis, however, revealed four phylogenetic groups within Milesina that also correlate with specific urediniospore characters (germ pore number and position and echinulation). These groups are proposed as new sections within Milesina (sections Milesina , Vogesiacae M. Scholler & Bubner, sect. nov. , Scolopendriorum M. Scholler & Bubner, sect. nov. and Carpaticae M. Scholler & Bubner, sect. nov. ). In addition, Milesinawoodwardiana Buchheit & M. Scholler, sp. nov. on Woodwardiaradicans , a member of the type section Milesina, is newly described. An identification key for European Milesina species, based on urediniospore features, is provided.
... This has motivated a diverse set of studies that have increased the knowledge on T. areolata, for example the range of alternate hosts , spore germination , infection on plantlets (Hietala, Solheim, & Fossdal, 2008) and management strategies such as cone bagging, or old cone removal (Kaitera, 2013;Kaitera & Tillman-Sutela, 2014;Kaitera et al., 2009a,b). Nonetheless, questions regarding the fungus' mode of reproduction and its impact on the management of the disease remain unanswered. ...
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Cherry spruce rust is a fungal disease of Norway spruce cones caused by Thekopsora areolata and responsible for significant losses in seed production in Sweden and Finland. Here, we report the first set of nine microsatellites, which will allow an effective genetic fingerprinting of T. areolata. The markers were isolated using the FIASCO method and were characterized using DNA from 49 single aecia sampled from spruce cones in three different seed orchards in Sweden. Eight of the nine markers were shown to be polymorphic among the aecia. The markers were unlinked and are therefore suitable for future population genetic studies.