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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Mycology and Nematology Genetic Diversity and Biology Laboratory » Research » Publications at this Location » Publication #330595

Title: Development of real-time and conventional PCR assays for identifying stubby root nematode Paratrichodorus allius

item HUANG, DANQIONG - North Dakota State University
item YAN, GUIPING - North Dakota State University
item Skantar, Andrea

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2017
Publication Date: 3/20/2017
Citation: Huang, D., Yan, G., Skantar, A.M. 2017. Development of real-time and conventional PCR assays for identifying stubby root nematode Paratrichodorus allius. Plant Disease. 101(6):964-972. doi: 10.1094/PDIS-10-16-1431-RE.

Interpretive Summary: Plant-parasitic nematodes are microscopic worms that attack plant roots and cause billions of dollars in economic losses to agriculture. The stubby root nematodes are an important group, not only for the damage they cause, but for transmitting the tobacco rattle virus responsible for corky ringspot disease on potato tubers. In this study, researchers from North Dakota State University along with an ARS scientist developed and validated conventional and high sensitivity diagnostic assays to identify a species of stubby root nematode when in isolation from soil or as part of complex soil communities of nematode species. These results are significant because they represent the first report of this particular stubby root nematode using high sensitivity molecular diagnostics to distinguish it from other nematode species. Scientists, extension agents and action agencies engaged in nematode research and control will use this research.

Technical Abstract: Paratrichodorus allius is an important pest on many crops, particularly, on potato due to its ability to transmit Tobacco rattle virus causing corky ringspot disease on tubers. Detection and identification of P. allius are important for effective disease management. In this study, a rapid and reliable molecular diagnosis of this nematode targeting ITS1 rDNA was established. The specificity of the designed primer was evaluated using 30 nematode species and results showed that a single amplicon was produced from DNA of P. allius only. Detection sensitivity analysis indicated that, an equivalent of 0.1 nematode could be detected by conventional PCR and an equivalent of 0.001 nematode by real-time PCR. Developed PCR assays successfully amplified DNA of stubby root nematodes isolated from 18 distinct soil samples in ND and MN, which were confirmed as P. allius by sequencing. The conventional PCR assay amplified target nematodes from complex nematode communities, supporting the success of this molecular diagnosis of P. allius. This is the first report of P. allius identification using real-time PCR method and from a nematode community with other nematodes using conventional PCR. The new PCR assays provide a rapid species identification strategy and are suitable for use in diagnostic laboratories and detection of field infestations with this nematode species.