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

Yan, Guiping and Smiley, Richard W. and Okubara, Patricia A. and Skantar, Andrea and Easley, Sandra A. and Sheedy, Jason G. and Thompson, Alison L. (2008) Detection and discrimination of Pratylenchus neglectus and P. thornei in DNA extracts from soil. Plant Disease, 92 (11). pp. 1480-1487. ISSN 0191-2917

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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: © 2008 The American Phytopathological Society. Published version deposited in accordance with the copyright policy of the publisher.
Faculty / Department / School: Historic - Faculty of Sciences - Department of Biological and Physical Sciences
Date Deposited: 30 Apr 2014 09:42
Last Modified: 29 Aug 2014 02:52
Uncontrolled Keywords: detection sensitivity; DNA extraction; DNA purification; lesion nematodes; PCR products; fungal species; lesion nematodes; PCR products; polymerase chain reaction methods; primer sets; Rrna genes
Fields of Research : 06 Biological Sciences > 0604 Genetics > 060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
05 Environmental Sciences > 0503 Soil Sciences > 050303 Soil Biology
07 Agricultural and Veterinary Sciences > 0703 Crop and Pasture Production > 070308 Crop and Pasture Protection (Pests, Diseases and Weeds)
Socio-Economic Objective: D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960413 Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments
Identification Number or DOI: 10.1094/PDIS-92-11-1480
URI: http://eprints.usq.edu.au/id/eprint/25131

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