Theoretical and Applied Genetics

, Volume 117, Issue 3, pp 343–352 | Cite as

Quantification of Fusarium solani f. sp. glycines isolates in soybean roots by colony-forming unit assays and real-time quantitative PCR

  • S. LiEmail author
  • G. L. Hartman
  • L. L. Domier
  • D. Boykin
Original Paper


Fusarium solani f. sp. glycines (FSG; syn. F. virguliforme Akoi, O’Donnell, Homma & Lattanzi) is a soil-borne fungus that infects soybean roots and causes sudden death syndrome (SDS), a widespread and destructive soybean disease. The goal of this study was to develop and use a real-time quantitative polymerase chain reaction (QPCR) assay to compare the accumulation of genomic DNA among 30 FSG isolates in inoculated soybean roots. Isolates differed significantly (P ≤ 0.05) in their DNA accumulation on a susceptible soybean cultivar when detected and quantified using a FSG-specific probe/primers set derived from the sequences of the nuclear-encoded, mitochondrial small subunit ribosomal RNA gene. QPCR results that were normalized as the fold change over the sample collection times after inoculation were significantly (P ≤ 0.001) correlated with the log10 transformed colony-forming unit (CFU) values of FSG obtained from plating of inoculated ground roots on FSG semi-selective agar medium. Several isolates were identified that accumulated more FSG DNA and had higher CFU values than the reference isolate FSG1 (Mont-1). Compared to other isolates, FSG5 was the most aggressive root colonizer based on DNA accumulation and CFU values in infested roots. The described QPCR assay should provide more specificity, greater sensitivity, and less variability than alternatives to the culturing-dependent and time-consuming plating assays. Evaluation of isolate relative DNA differences on host plants using the QPCR approach provides useful information for evaluating isolates based on the extent and/or degree of colonization on soybean roots and for selecting isolates for breeding SDS-resistant soybean lines.


Colony Form Unit Quantitative Polymerase Chain Reaction Soybean Root Sudden Death Syndrome Colony Form Unit Count 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank L. Achenbach, S. Abney, T. Anderson, L. Gray, J. Kurl, T. Niblack, J. Rupe, K. O’Donnell, and X. B. Yang for providing fungal cultures or diseased plants for fungal isolation; and undergraduate students, J. King, X. Zeng, N. Weaterspoon, Ryan DuBrall, and C. You for assisting in this project. We also thank the senior editor and anonymous reviewers for a thorough review of the manuscript. This research was partially supported by grants from the United Soybean Board, Illinois Soybean Association, North Central Soybean Research Program, and USDA-ARS and CSREES. Trade and manufacturers names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of products to the exclusion of others that may also be suitable.


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • S. Li
    • 1
    Email author
  • G. L. Hartman
    • 2
  • L. L. Domier
    • 2
  • D. Boykin
    • 3
  1. 1.United States Department of Agriculture-Agricultural Research Service (USDA-ARS)Crop Genetics & Production Research UnitStonevilleUSA
  2. 2.Department of Crop SciencesUSDA-ARS, Soybean/Maize Germplasm, Pathology, and Genetics Research UnitUrbanaUSA
  3. 3.USDA-ARSStonevilleUSA

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