SCAR–based PCR primers to detect the hybrid pathogen Phytophthora alni and its subspecies causing alder disease in Europe

Ioos, Renaud; Husson, Claude; Andrieux, Axelle; Frey, Pascal

doi:10.1007/s10658-005-6233-2

Cited by 39 publications

(36 citation statements)

References 30 publications

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“…Paa has been found in Ireland, UK, Sweden, Germany, Netherlands, Belgium, France, Spain, Poland, Czech Republic, Austria, and Hungary up to the present time (Szabó et al 2000;Nagy et al 2003;Brasier et al 2004;De Merlier et al 2005;Ioos et al 2005;Cerny et al 2008;Pintos Varela et al 2010;Solla et al 2010;Trzewik & Orlikowska 2010). The distribution area of Paa overlaps the area of Pam in the West (UK and northwestern part of continental Europe) and the area of Pau in almost the whole continental Europe.…”

Section: Discussionmentioning

confidence: 93%

“…The distribution area of Paa overlaps the area of Pam in the West (UK and northwestern part of continental Europe) and the area of Pau in almost the whole continental Europe. According to the fact that Paa is a hybrid of Pam and Pau (Ioos et al 2005(Ioos et al , 2006Bakonyi et al 2007;Érsek & Nagy 2008), Paa may have its origin somewhere in northwestern continental Europe − in the area of coincidence of both, Pau and Pam. Although Pau has recently been much less frequent than Paa (Brasier et al 2004), it has the most extensive area -it is known from Sweden, Lithuania, Germany, Netherlands, Belgium, France, Spain, Czech Republic, Austria, Italy, Hungary, and Slovenia (Szabó et al 2000;Santini et al 2001;Nagy et al 2003;Brasier et al 2004;De Merlier et al 2005;Ioos et al 2005;Munda et al 2006;Pintos Varela et al 2012).…”

Section: Discussionmentioning

confidence: 99%

“…Reliable PCR methods for subspecies identification were developed in previous years. Two methods were based on anonymous RAPD markers (Ioos et al 2005;Bakonyi et al 2006), another approach (Ioos et al 2006) was targeted on introns in four nuclear orthologous genes and distribution of single allele within the genome of P. alni individuals. The development of a reliable identification method enabled to study the distribution of subspecies and their ecological preferences.…”

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confidence: 99%

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Identification of Phytophthora alni subspecies in riparian stands in the Czech Republic

Štěpánková¹,

Černý²,

Strnadová³

et al. 2013

Plant Prot. Sci.

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AbstractŠtěpánková P., Černý K., Strnadová V., Hanáček P., Tomšovský M. (2013): Identification of Phytophthora alni subspecies in riparian stands in the Czech Republic. Plant Protect. Sci., 49 (Special Issue): S3-S10.In the Czech Republic, Phytophthora alni was first confirmed in 2001 and the pathogen has been quickly spreading and occupying almost the whole area of the country. The pathogen attacks Alnus glutinosa or A. incana to a lesser extent and causes considerable losses of alder trees along hundreds of kilometres of riverbanks. The aim of our work was to perform the identification of P. alni isolates at the subspecific level using PCR and to determine the frequencies and distribution of particular subspecies. The allele-specific PCR primers focused on allele diversity of orthologs of ASF-like, TRP1, RAS-Ypt, and GPA1 genes were selected for identification. Eighty-eight per cent of the 59 analysed isolates belonged to P. alni ssp. alni while 12% were P. alni ssp. uniformis. P. alni ssp. multiformis has not been recorded in the country till now. The two subspecies differed in distribution. P. alni ssp. alni dominated in riparian stands along broader rivers in lowlands and the results confirmed the more effective spreading of P. alni ssp. alni based on its higher aggressiveness and ecological advantage. P. alni ssp. uniformis was acquired rather from riparian stands of small watercourses at higher altitudes. The insular distribution of P. alni ssp. uniformis may represent the remains of its former occurrence. Therefore, P. alni ssp. uniformis may be an indigenous subspecies suppressed by the more aggressive related taxon.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Identification of Phytophthora alni subspecies in riparian stands in the Czech Republic

Štěpánková¹,

Černý²,

Strnadová³

et al. 2013

Plant Prot. Sci.

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“…To date, skim milk has been widely employed as an additive for the extraction of DNA from diverse environmental samples including oil-contaminated soil 29) , chemically polluted soil 46) , coral reef sediments 10) , groundwater 7) , woody tissues 24) and stone samples 37) . Moreover, the DNA obtained using methodologies that employ skim milk as an additive has been used in a series of studies for the detection of specific organisms 6,9,24,25,28,33,36,37,43,45) and genes 29,38) in a variety of environments.…”

mentioning

confidence: 99%

“…Moreover, the DNA obtained using methodologies that employ skim milk as an additive has been used in a series of studies for the detection of specific organisms 6,9,24,25,28,33,36,37,43,45) and genes 29,38) in a variety of environments. Such DNA preparations have also been used in microbial community analyses in several reports 7,10,14,15,26,42,46) .…”

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confidence: 99%

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

et al. 2008

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A series of additives were evaluated for their effects on improving the yield and quality of DNA extracted from recalcitrant soils. Levels of possible DNA contaminants in these supplements were also assessed. Three of the additives (skim milk, casein, and RNA) were shown to be effective in improving the stable extraction of DNA from recalcitrant samples of Andosol. However, whereas skim milk appeared to be the most effective additive for this purpose, our data indicated that this commercially sourced product contained considerable amounts of contaminant DNA (30 to 40 µg/g skim milk). A ribosomal intergenic spacer analysis (RISA) revealed the consistent contamination of different batches of this product with DNA of several species of both eukaryotes (cattle and protists) and prokaryotes. In particular, thermophilic bacteria such as Geobacillus and Anoxybacillus were identified in the sequenced PCR amplicons from skim milk. The results of the RISA clearly also indicated that the impact of contaminated DNA on the analysis of a microbial community could be significant when skim milk is used for extracting DNA from a recalcitrant soil. In contrast, only a trace amount of contaminating DNA was evident in casein and none was detected in the RNA examined in the present study.

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ChemInform Abstract: Preparation of Fungal Specimens for Direct Molecular Applications

et al. 2010

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SCAR–based PCR primers to detect the hybrid pathogen Phytophthora alni and its subspecies causing alder disease in Europe

Cited by 39 publications

References 30 publications

Identification of Phytophthora alni subspecies in riparian stands in the Czech Republic

Identification of Phytophthora alni subspecies in riparian stands in the Czech Republic

Evaluation of the Effects of Different Additives in Improving the DNA Extraction Yield and Quality from Andosol

ChemInform Abstract: Preparation of Fungal Specimens for Direct Molecular Applications

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