Development of a Droplet Digital PCR Assay for Detection and Quantification of Stubby Root Nematode, Paratrichodorus allius, in Soil

The stubby root nematode Paratrichodorus allius is an important plant-parasitic nematode species within the Trichodoridae family. It can directly harm the plants by feeding on the roots or indirectly by transmitting Tobacco rattle virus. These nematodes are mostly diagnosed either by traditional microscopic methods or a polymerase chain reaction (PCR)-based method. Droplet digital PCR (ddPCR) is a novel PCR technique which is sensitive and precise in quantifying DNA templates of the test samples. In this study, we developed a ddPCR assay to detect and quantify P. allius in soil. The specificity and sensitivity of the assay was first determined using P. allius nematode DNA or DNA from sterilized soil artificially inoculated with P. allius, and the assay was used to quantify P. allius populations in field soils. The assay did not detect nematodes other than P. allius, thus showing high specificity. It was able to detect P. allius equivalent to a 0.01 and 0.02 portion of a single nematode in soil DNA and nematode DNA extracts, respectively. Highly linear relationships between DNA copy numbers from ddPCR and serial dilutions of known concentrations were observed with DNA from P. allius nematodes (R2 = 0.9842) and from artificially infested soil (R2 = 0.9464). The P. allius populations from field soils determined by ddPCR were highly correlated with traditional microscopic counts (R2 = 0.7963). To our knowledge, this is the first report of applying ddPCR to detect and quantify stubby root nematode in soil. The results of this study support the potentiality of a ddPCR assay as a new research tool in diagnostics of plant-parasitic nematodes.

Rapid Detection of Tobacco Rattle Tobravirus in Viruliferous Paratrichodorus allius from Greenhouse and Field Specimens

The stubby root nematode, Paratrichodorus allius, is important to the potato industry in the Pacific Northwest of USA, because it vectors Tobacco rattle virus (TRV), the causal agent of corky ringspot disease. The current method for determining if nematodes are viruliferous for TRV takes several weeks, requiring a glasshouse bioassay followed by a serological test. To overcome this drawback, a rapid and affordable molecular test was developed using reverse transcription polymerase chain reaction (RT-PCR) to identify viruliferous P. allius nematodes within 48 hours. Primers from the 16 kDa gene of TRV were used to detect TRV in both greenhouse-reared and field collected P. allius. TRV RNA can be detected consistently in nucleic acids equivalent to one quarter of a viruliferous adult nematode reared in the greenhouse. In order to reduce the time and expense of processing individual nematodes from field samples, viral RNA was consistently and affordably detected in extracts from 5 field-collected adult P. allius.

Survey of crop losses in response to phytoparasitic nematodes in the United States for 1994

Previous reports of crop losses to plant-parasitic nematodes have relied on published results of survey data based on certain commodities, including tobacco, peanuts, cotton, and soybean. Reports on crop-loss assessment by land-grant universities and many commodity groups generally are no longer available, with the exception of the University of Georgia, the Beltwide Cotton Conference, and selected groups concerned with soybean. The Society of Nematologists Extension Committee contacted extension personnel in 49 U.S. states for information on estimated crop losses caused by plant-parasitic nematodes in major crops for the year 1994. Included in this paper are survey results from 35 states on various crops including corn, cotton, soybean, peanut, wheat, rice, sugarcane, sorghum, tobacco, numerous vegetable crops, fruit and nut crops, and golf greens. The data are reported systematically by state and include the estimated loss, hectarage of production, source of information, nematode species or taxon when available, and crop value. The major genera of phytoparasitic nematodes reported to cause crop losses were Heterodera, Hoplolaimus, Meloidogyne, Pratylenchus, Rotylenchulus, and Xiphinema.

Management of Paratrichodorus allius Damage to Onion in the Columbia Basin of Oregon

Production of storage and dehydration (dehy) onions is increasing rapidly in the northcentral Oregon region of the Columbia Basin. Roughly circular patches of stunted onions have been observed in many fields and are often numerous and (or) extensive in area. Onions in these patches often exhibit symptoms typical of stubby-root nematodes, and Paratrichodorus allius has been collected from several damaged areas. This study examined the relationship of P. allius densities to onion yield reduction and benefit from oxamyl application. Transect samples and onions harvested across areas with varying P. allius densities revealed that the total number of onions was not affected by P. allius but that onions were in smaller, less valuable size classes. Yield of the largest size class of storage onions (colossals) declined substantially (57-61%) even at low (5-16/250 g soil) nematode densities. Treatment with oxamyl at 1.1 kg a.i./ha mitigated most of the damage, and the value of both storage and dehy onions was increased by more than $1,200/ha. Early applications were superior to later applications, whereas treatment at both times was no better than the early treatment alone. Damage at low (<10/250 g soil) nematode densities, low treatment cost ($86-172/ha), and high crop values suggest an economic benefit from treatment at population densities of four or more P. allius/250 g soil. However, stunted patches of onions may occur for reasons other than nematodes, and the presence of P. allius should be confirmed before treating fields. This is the first report of stubby-root nematode damage to dehy onions and to storage onions in the Columbia Basin.