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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Publications at this Location » Publication #219799

Title: Detection of Phakopsora pachyrhizi Spores in Rain Using a Real-Time PCR Assay

item Szabo, Les

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2008
Publication Date: 4/1/2009
Citation: Barnes, C.W., Szabo, L.J., Bowersox, V.C. 2009. Detection of Phakopsora pachyrhizi Spores in Rain Using a Real-Time PCR Assay. Phytopathology. 99:328-338.

Interpretive Summary: Asian soybean rust, caused by the rust fungus Phakopsora pachyrhizi, was first reported in the U.S. in 2004 and poses a serious threat to soybean production. Asian soybean rust, as well as other rust diseases, is commonly spread by aerial transport of spores. Rust spores can travel long distances and are deposited by rain. Development of a national monitoring system based on detection of fungal spores in rain would provide as an early warning system for the spread of this disease. Weekly precipitation samples were assayed using a DNA based assay (PCR) from 120 and 110 National Atmospheric Deposition Program (NADP) sites to map the deposition of P. pachyrhizi spores in the soybean growing regions of the US, during the growing season of 2005 and 2006, respectively. The results of the study show that P. pachyrhizi can be detected in rain, and that the spores are deposited through out the U.S. soybean growing regions. P. pachyrhizi spores were detected from May through October. There was a 3-fold increase in the frequency of detection from 2005 to 2006, and an increase in the number of spores per sample. This study demonstrates that use of a DNA based assay to detect spores in rain collected at geographically dispersed NADP sites can serve as a powerful tool for monitoring the movement of P. pachyrhizi. Scientists and agricultural specialists will use the data developed by this monitoring system to improve field scouting programs and development of disease management recommendations for farmers. Scientists will use this approach to monitoring the movement of other plant pathogens dispersed in the atmosphere.

Technical Abstract: Transport of rust fungal spores along the Puccinia Pathway has been well recognized. In 2005 and 2006, rain was collected weekly from May-August at 112 selected National Atmospheric Deposition Program/ National Trends Network sites across the soybean growing region of the central and eastern US. Rain samples were screened for Phakopsora pachyrhizi (causal agent of Asian soybean rust) DNA using a nested real-time PCR assay. The time to process a rain sample, from the date a sample was collected until it was assayed, was less than three weeks. To date, P. pachyrhizi spores have been detected in every state in the study, but more frequently in states along the Gulf and Atlantic coasts and along the Ohio River Valley westward to Kansas. A bimodal temporal distribution of samples testing positive for P. pachyrhizi was found in both years. However, there was a greater than three-fold increase in the number of samples testing positive for P. pachyrhizi in 2006 than 2005, with the most significant increase in August. There was also an increase in the average spore load per sample in 2006 compared to 2005. Sequence analysis of a subset of positive rain samples was used to validate the assay results. From the sequence analysis, two polymorphic regions were found resulting in five distinct genotypes among the 52 sequenced amplicons. One genotype was found in 54% of the samples tested, while the other genotypes were found less frequently.