Detection and discrimination of Pratylenchus neglectus and P. thornei in DNA extracts from soil

Article

Yan, Guiping, Smiley, Richard W., Okubara, Patricia A., Skantar, Andrea, Easley, Sandra A., Sheedy, Jason G. and Thompson, Alison L.. 2008. "Detection and discrimination of Pratylenchus neglectus and P. thornei in DNA extracts from soil." Plant Disease: an international journal of applied plant pathology. 92 (11), pp. 1480-1487. https://doi.org/10.1094/PDIS-92-11-1480
Article Title

Detection and discrimination of Pratylenchus neglectus and P. thornei in DNA extracts from soil

ERA Journal ID2647
Article CategoryArticle
AuthorsYan, Guiping (Author), Smiley, Richard W. (Author), Okubara, Patricia A. (Author), Skantar, Andrea (Author), Easley, Sandra A. (Author), Sheedy, Jason G. (Author) and Thompson, Alison L. (Author)
Journal TitlePlant Disease: an international journal of applied plant pathology
Journal Citation92 (11), pp. 1480-1487
Number of Pages8
Year2008
Place of PublicationSt. Paul, MN. United States
ISSN0191-2917
1943-7692
Digital Object Identifier (DOI)https://doi.org/10.1094/PDIS-92-11-1480
Abstract

A species-specific polymerase chain reaction (PCR) method was developed to detect and identify the root-lesion nematodes Pratylenchus neglectus and P. thornei from soil. A primer set was designed from Pratylenchus 28S rRNA gene sequences of the D3 expansion domain. Primer specificity was confirmed with 23 isolates of 15 nematode species and other plant-parasitic and non-plant-parasitic nematodes typically present in the soil communities, and with six fungal species commonly associated with wheat root rot. DNA obtained using a commercially available kit and a method developed in our laboratory gave comparable amplification. PCR conditions were optimized and the two species were differentiated by PCR products of 144 bp for P. neglectus and 288 bp for P. thornei. With this assay, we detected a single juvenile in 1 g of sterile, inoculated soil. Examination of 30 field soil samples revealed that this method was applicable to a range of soils naturally infested with these two pathogens in Oregon. This PCR-based method is rapid, efficient, and reliable, does not require expertise in nematode taxonomy and morphology, and could be used as a rapid diagnostic tool for commercial and research applications for disease forecasting and management.

Keywordsdetection sensitivity; DNA extraction; DNA purification; lesion nematodes; PCR products; fungal species; lesion nematodes; PCR products; polymerase chain reaction methods; primer sets; Rrna genes
ANZSRC Field of Research 2020310506. Gene mapping
410603. Soil biology
300409. Crop and pasture protection (incl. pests, diseases and weeds)
Public Notes

© 2008 The American Phytopathological Society. Published version deposited in accordance with the copyright policy of the publisher.

Byline AffiliationsOregon State University, United States
Department of Agriculture, United States
Institution of OriginUniversity of Southern Queensland
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