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United States Department of Agriculture

Agricultural Research Service


Location: Soybean/maize Germplasm, Pathology, and Genetics Research

Title: Detection of Low Numbers of Phakopsora pachyrhizi Spores by Quantitative Real-Time PCR)

item Steinlage, T
item Miles, Monte
item Isard, S
item Marois, J
item Hartman, Glen

Submitted to: National Soybean Rust Symposium
Publication Type: Abstract only
Publication Acceptance Date: 7/29/2006
Publication Date: 8/2/2006
Publication URL:
Citation: Steinlage, T.A., Miles, M.R., Isard, S.A., Marois, J., Hartman, G.L. 2006. Detection of Low Numbers of Phakopsora pachyrhizi Spores by Quantitative Real-Time PCR. National Soybean Rust Symposium. Availabe at:

Interpretive Summary:

Technical Abstract: One important aspect of an early detection and monitoring system for soybean rust is the reliability of detection of low spore numbers from traps. Microscopic examination of slides is time-consuming, and may provide inaccurate results due to look-alike spores (spores of a similar size, morphology, and color). PCR based technologies offer the opportunity for rapid, definitive confirmation of suspect spores. Groups of spores (0, 1, 4, 8, 16, and 100) were removed from Vaseline-coated slides with a scalpel, and DNA was extracted by the FastDNA protocol. Detection was performed by quantitative real-time PCR. When 100 or 16 spores were extracted, detection was achieved with every sample. At lower levels of 8, 4, and 1 spores extracted, detection was achieved in 75%, 88%, and 38% of the samples, respectively. No false positives occurred in the negative controls. During the 2006 field season this technology was applied to spore traps in Florida. Over 800 samples were processed with 44 slide traps and 17 rainwater traps yielding positive signals for P. pachyrhizi. This technology shows promise as a method for confirming the identification of suspect spores, and may aid in future early warning systems. Additional experimentation is on-going to improve the accuracy of detection when spore numbers are low.

Last Modified: 8/24/2016
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