Title page for ETD etd-04192012-180014

Type of Document Master's Thesis
Author Rush, Tomas Allen
Author's Email Address trush2@lsu.edu
URN etd-04192012-180014
Title Searching for Alternative Hosts and Determining the Variation in the Internal Transcribed Spacer (ITS) Region of Phakopsora pachyrhizi and the Implications for Currently Used Molecular Diagnostic Assays.
Degree Master of Science (M.S.)
Department Plant Pathology & Crop Physiology
Advisory Committee
Advisor Name Title
Aime, M. Catherine Committee Chair
Schneider, Raymond W. Committee Co-Chair
Urbatsch, Lowell Committee Member
  • Integrated Pest Management (IPM)
  • Phakopsora tecta
  • Quantitative PCR
Date of Defense 2012-02-24
Availability unrestricted
Phakopsora pachyrhizi, the causal agent of soybean rust (SBR), is a serious disease on soybeans.The objectives of this project were to identify additional alternative and possible overwintering hosts of the SBR pathogen and to validate the current detection assays for SBR. For the first objective, we attempted to identify naturalized Louisiana legume(s) that can serve as hosts and overwintering sites for P. pachyrhizi. It was theorized that New Iberia and Iberville Parishes in south Louisiana are usually the first locations of soybean infection in the spring. This suggests that there may be alternative leguminous hosts located in these parishes that may serve as overwintering hosts for P. pachyrhizi. Over 100 species of naturalized legumes were tested in field experiments to identify susceptible alternative hosts of the pathogen from November to May. For the second project, samples of P. pachyrhizi were collected from different parishes across Louisiana and sequenced across the ITS locus.These sequences were analyzed for variability within the locus and compared to the standard used in the current assay for pathogen detection. The Frederick et al. (2002) assay discriminates between P. pachyrhizi and P. meibomiae, a closely related mildly virulent species on soybeans in the US. A second assay, Barnes et al. (2009), was designed to detect a single spore of P. pachyrhizi in rain wash material, to monitor spore deposition and predict the movement of SBR in major soybean-producing states. However, the Barnes et al. (2009) assay has been shown to produce false positive and false negative results when used to detect the presence of P. pachyrhizi in North America. We tested five other Phakopsora spp. by both assays and found that only the Barnes et al. (2009) assay was able to detect all other Phakopsora spp. that were tested. Furthermore, the DNA segments used in the Barnes et al. (2009) assay, the primers had base pairs similarities that were 100% with other Phakopsora spp. and more than 60% with the specific P. pachyrhizi probe. In addition, we had determine that neither assay was placed in variable regions of the ITS locus.
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