Development and application of a PCR-based 'molecular tool box' for the identification of Phytophthora species damaging forests and natural ecosystems

Plant Pathology

Volumn 57, Issue 1, 2008, Pages 64-75

  Schena, L ^a   Duncan, J M ^b   Cooke, D E L ^b  

^a UNIVERSITY MEDITERRANEA OF REGGIO CALABRIA   (Italy)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

Author keywords

Forests and natural ecosystems; Molecular tool box; Phytophthora spp.; Ras related protein gene; Ypt1 gene

Indexed keywords

DETECTION METHOD; DNA; ECOSYSTEM APPROACH; FOREST ECOSYSTEM; FUNGUS; GENE EXPRESSION; GENETIC ANALYSIS; IDENTIFICATION METHOD; PARASITE; POLYMERASE CHAIN REACTION; PROTEIN; SENSITIVITY ANALYSIS; TAXONOMY;

ENGLAND; EURASIA; EUROPE; SCOTLAND; UNITED KINGDOM; WALES; WESTERN EUROPE;

PHYTOPHTHORA; PHYTOPHTHORA CACTORUM; PHYTOPHTHORA CAMBIVORA; PHYTOPHTHORA CINNAMOMI; PHYTOPHTHORA CITRICOLA; PHYTOPHTHORA EUROPAEA; PHYTOPHTHORA IDAEI; PHYTOPHTHORA ILICIS; PHYTOPHTHORA INUNDATA; PHYTOPHTHORA KERNOVIAE; PHYTOPHTHORA LATERALIS; PHYTOPHTHORA MEGASPERMA; PHYTOPHTHORA NEMOROSA; PHYTOPHTHORA PSEUDOSYRINGAE; PHYTOPHTHORA PSYCHROPHILA; PHYTOPHTHORA QUERCINA; PHYTOPHTHORA RAMORUM; PYTHIUM;

EID: 38349011349     PISSN: 00320862     EISSN: 13653059     Source Type: Journal    
DOI: 10.1111/j.1365-3059.2007.01689.x     Document Type: Article

References (45)

1. Böhm J, Hahn A, Schubert R, et al., 1999. Real-time quantitative PCR: DNA determination in isolated spores of the mycorrhizal fungus Glomus mosseae and monitoring of Phytophthora infestans and Phytophthora citricola in their respective host plants. Journal of Phytopathology 147, 409 16.
2. Brasier C, Denman S, Brown A, Webber J, 2004a. Sudden oak death (Phytophthora ramorum) discovered on trees in Europe. Mycological Research 108, 1107 10.
3. Brasier CM, Cooke DEL, Duncan JM, 1999. Origin of a new Phytophthora pathogen through interspecific hybridization. Proceedings of the National Academy of Sciences, USA 96, 5878 83.
4. Brasier CM, Sánchez-Hernandez E, Kirk SA, 2003. Phytophthora inundata sp. nov., a part heterothallic pathogen of trees and shrubs in wet or flooded soils. Mycological Research 107, 477 84.
5. Brasier CM, Kirk SA, Delcan J, Cooke DEL, Jung T, Man In't Veld WA, 2004b. Phytophthora alni sp. nov. and its variants: designation of emerging heteroploid hybrid pathogens spreading on Alnus trees. Mycological Research 108, 1172 84.
6. Brasier CM, Beales PA, Kirk SA, Denman S, Rose J, 2005. Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in Britain. Mycological Research 109, 853 9.
7. Brown AV, Brasier CM, 2007. Colonization of tree xylem by Phytophthora ramorum, P. kernoviae and other Phytophthora species. Plant Pathology 56, 227 41.
8. Causin R, Scopel C, Grendene A, Montecchio L, 2005. An improved method for the detection of Phytophthora cactorum (L.C.) Schröeter in infected plant tissues using SCAR markers. Journal of Plant Pathology 87, 25 35.
9. Chen Y, Roxby R, 1996. Characterization of a Phytophthora infestans gene involved in the vesicle transport. Gene 181, 89 94.
10. Coakley SM, Scherm H, Chakraborty S, 1999. Climate change and plant disease management. Annual Review of Phytopathology 37, 399 426.
11. Coelho AC, Cravador A, Bollen A et al., 1997. Highly specific and sensitive non-radioactive molecular identification of Phytophthora cinnamomi. Mycological Research 101, 1499 507.
12. Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM, 2000. A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genetics and Biology 30, 17 32.
13. Cooke DEL, Jung T, Williams NA, Schubert R, Oßwald W, Duncan JM, 2005. Genetic diversity of European populations of the oak fine-root pathogen Phytophthora quercina. Forest Pathology 35, 57 70.
14. Cooke DEL, Schena L, Cacciola SO, 2007. Tools to detect, identify and monitor Phytophthora species in natural ecosystems. Journal of Plant Pathology 89, 13 28.
15. Cullen DW, Lees AK, Toth IK, Duncan JM, 2001. Conventional PCR and real-time quantitative PCR detection of Helminthosporium solani in soil and potato tubers. European Journal of Plant Pathology 107, 387 98.
16. De Merlier D, Chandelier A, Debruxelles N, et al., 2005. Characterization of alder Phytophthora isolates from Wallonia and development of SCAR primers for their specific detection. Journal of Phytopathology 153, 99 107.
17. Hansen EM, Reeser PW, Davidson JM, et al., 2003. Phytophthora nemorosa, a new species causing cankers and leaf blight of forest trees in California and Oregon, USA. Mycotaxon 88, 129 38.
18. Hayden KJ, Rizzo D, Tse J, Garbelotto M, 2004. Detection and quantification of Phytophthora ramorum from California forests using a real-time polymerase chain reaction assay. Phytopathology 94, 1075 83.
19. Hughes KJD, Griffin RL, Tomlinson JA, Boonham N, Inman AJ, Lane CR, 2006. Development of a one-step real-time PCR assay for diagnosis of Phytophthora ramorum. Phytopathology 96, 975 81.
20. Ioos R, Husson C, Andrieux A, Frey P, 2005. SCAR-based PCR primers to detect the hybrid pathogen Phytophthora alni and its subspecies causing alder disease in Europe. European Journal of Plant Pathology 112, 323 35.
21. Ioos R, Laugustin L, Schenck N, Rose S, Husson C, Frey P, 2006. Usefulness of single copy genes containing introns in Phytophthora for the development of detection tools for the regulated species P. ramorum and P. fragariae. European Journal of Plant Pathology 116, 171 6.
22. Ippolito A, Schena L, Soleti Logorio V, Yaseen T, Nigro F, 2004. Real-time detection of Phytophthora nicotianae and P. citrophthora in citrus roots and soils. European Journal of Plant Pathology 110, 833 43.
23. Ivors K, Garbelotto M, Vries IDE, et al., 2006. Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations. Molecular Ecology 15, 1493 505.
24. Jung T, Blaschke H, Oßwald W, 2000. Involvement of soilborne Phytophthora species in Central European oak decline and the effect of site factors on the disease. Plant Pathology 49, 706 18.
25. Jung T, Hansen EM, Winton L, Oßwald W, Delatour C, 2002. Three new species of Phytophthora from European oak forests. Mycological Research 106, 397 411.
26. Jung T, Nechwatal J, Cooke DEL, et al., 2003. Phytophthora pseudosyringae sp. nov., a new species causing root and collar rot of deciduous tree species in Europe. Mycological Research 107, 772 89.
27. Jung T, Hudler GW, Jensen-Tracy SL, Griffiths HM, Fleischmann F, Osswald W, 2005. Involvement of Phytophthora species in the decline of European beech in Europe and the USA. Mycologist 19, 159 66.
28. Jurskis V, 2005. Eucalypt decline in Australia, and a general concept of tree decline and dieback. Forest Ecology and Management 215, 1 20.
29. Kong P, Hong CX, Richardson PA, 2003. Rapid detection of Phytophthora cinnamomi using PCR with primers derived from the Lpv putative storage protein genes. Plant Pathology 52, 681 93.
30. Kroon LPNM, Bakker FT, van den Bosch GBM, Bonants PJM, Flier WG, 2004. Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genetics and Biology 41, 766 82.
31. Luque J, Parladé J, Pera J, 2002. Seasonal changes in susceptibility of Quercus suber to Botryosphaeria stevensii and Phytophthora cinnamomi. Plant Pathology 51, 338 45.
32. Martin FN, Tooley PW, 2003. Phylogenetic relationships of Phytophthora ramorum, P. nemorosa, and P. pseudosyringae, three species recovered from areas in California with sudden oak death Mycological Research 107, 1379 91.
33. Martin FN, Tooley PW, Blomquist C, 2004. Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material. Phytopathology 94, 621 31.
34. Nechwatal J, Schlenzing A, Jung T, Cooke DEL, Duncan JM, Oßwald WF, 2001. A combination of baiting and PCR techniques for the detection of Phytophthora quercina and P. citricola in soil samples from oak stands. Forest Pathology 31, 85 97.
35. Rizzo DM, Garbelotto M, Hansen EM, 2005. Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests. Annual Review of Phytopathology 43, 309 35.
36. Rozen S, Skaletsky HJ, 2000. Primer 3 on the WWW for general users and for biologist programmers. In : Krawetz S, Misener S, eds. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ, USA : Humana Press, 365 86.
37. Schena L, Cooke DEL, 2006. Assessing the potential of regions of the nuclear and mitochondrial genome to develop a 'molecular tool box' for the detection and characterization of Phytophthora species. Journal of Microbiological Methods 67, 70 85.
38. Schena L, Nigro F, Ippolito A, Gallitelli D, 2004. Real-time quantitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. European Journal of Plant Pathology 110, 893 908.
39. Schena L, Hughes KJD, Cooke DEL, 2006. Detection and quantification of Phytophthora ramorum, P. kernoviae, P. citricola, and P. quercina in symptomatic leaves by multiplex real-time PCR. Molecular Plant Pathology 7, 365 79.
40. Schubert R, Bahnweg G, Nechwatal J, et al., 1999. Detection and quantification of Phytophthora species which are associated with root-rot diseases in European deciduous forests by species-specific polymerase chain reaction. Forest Pathology 29, 169 88.
41. Tooley PW, Kyde KL, Englander L, 2004. Susceptibility of selected ericaceous ornamental host species to Phytophthora ramorum. Plant Disease 88, 993 9.
42. Tooley PW, Martin FN, Carras MM, Frederick RD, 2006. Real-time fluorescent polymerase chain reaction detection of Phytophthora ramorum and Phytophthora pseudosyringae using mitochondrial gene regions. Phytopathology 96, 336 45.
43. Vettraino AM, Barzanti GP, Bianco MC, et al., 2002. Occurrence of Phytophthora species in oak stands in Italy and their association with declining oak trees. Forest Pathology 32, 19 28.
44. Vettraino AM, Morel O, Perlerou C, Robin C, Diamandis S, Vannini A, 2005. Occurrence and distribution of Phytophthora species in European chestnut stands, and their association with ink disease and crown decline. European Journal of Plant Pathology 111, 169 80.
45. Winton LM, Hansen EM, 2001. Molecular diagnosis of Phytophthora lateralis in trees, water, and foliage baits using multiplex polymerase chain reaction. Forest Pathology 31, 275 83.