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United States Department of Agriculture

Agricultural Research Service

2008 Annual Report

1a.Objectives (from AD-416)
The long-term objective of this project is to develop a stable, biologically relevant taxonomy for the genus Alternaria with particular reference to the small-spored members of the genus, which are the taxa most often involved in phytosanitary issues and which are also frequently misidentified. Associated with this objective is the development of molecular protocols for detection and identification of target species of phytosanitary importance that are based upon the systematics work. Certain species of Alternaria (e.g., A. gaisen, A. yaliinficiens) are currently known to have a limited geographic distribution that restricts the movement of deciduous tree fruit to the U.S. and other world markets. Other species, many of which are undescribed or frequently misidentified, occur in the United States and in other countries, and need to be characterized and described so that regulatory actions regarding Alternaria on intercepted plant products can be based upon a firm and scientific understanding of the Alternaria taxa that occur on tree fruits and other substrates in the U.S. Over the next 5 years we will focus on the following objective: Objective 1: Isolate and accumulate sequence data from genomic transcripts of known Alternaria spp. which are detected during development of phenotypic traits that vary among different sub-generic groups sensu Simmons and Roberts (1993) and species within those groups, with particular emphasis on sporulation pattern, conidial morphology and, if necessary, germination-mediated metabolite production.

1b.Approach (from AD-416)
A fundamental understanding of species-diversity (identity) among Alternaria strains associated with tree fruit will be developed using morphological characters and species-specific DNA sequences identified via subtractive hybridization protocols. Research will be conducted as necessary to address market- or issue-specific questions that arise from interactions with trading partners. Replacing 5350-22000-014-00D (11/03).

3.Progress Report
Activities for this project address Problem Statement 1B: Detection, Identification, Characterization, and Classification of Pathogens in the NP 303 Action Plan. Within this problem statement, three sub-problems most accurately describe the current and future research efforts within the CRIS. 1. Although accurately classifying pathogens is important for understanding disease etiology, transmission, and control, the systematics of plant pathogens is plagued by large gaps in knowledge about specific groups of pathogens. 2. Because agricultural globalization has expanded, the need for taxonomic and other biological knowledge of foreign pathogens similarly has increased. 3. Because new molecular approaches may yield accurate tests only when developed within a sound systematic framework, such method development will also require complementary morphological research.

Blind experiments were completed that validated the use of the modified environmental chambers for morphological differentiation of various species of Alternaria that produce distinct patterns of sporulation in culture. Training and method development began for using selective subtractive hybridization to discover species-specific mRNA, creating cDNA libraries from the subtracted RNA, and evaluating specificity of cloned sequenced contained in the cDNA libraries. Additionally, method development for using the modified environmental chambers to grow dark- and light-induced cultures of Alternaria was completed. Initially, A. alternata and A. gaisen were used as tester and driver in the subtractive hybridization experiments, but unambiguously specific subtracted clones were not found. Subtractions were reinitiated using only dark- and light-grown A. gaisen in order to identify sporulation-specific mRNA and to refine the methodology that is specific for Alternaria.

1. Two new species in the fungal genus Alternaria were described. The fungal species Alternaria is important in crop disease and new species have yet to be identified and described. Alternaria species, A. roseogrisea R.G. Roberts and A. undulata R.G. Roberts were described from sunflower seeds and Australian navel oranges, respectively. ARS scientists in Wenatchee, WA found that these newly published species descriptions contribute incrementally to the list of known species and in the case of A. undulata, describe its association with a previously unrecognized disease of imported navel oranges. This information will be useful to plant quarantine regulatory agencies and to other scientists. This addressed National Program 303, Component 1, Problem 1b.

2. U.S. third party submission for WT/DSB 367. Fire blight import regulations proposed by Australia ofr the United States and New Zealand apples is not science-based. Both the New Zealand first party submission and the U.S. third party submission relied heavily upon a revised risk assessment published in 2008 (See #1 under publications). This revised risk assessment estimated the risk to an importing country of importing the fire blight bacterium Erwinia amylovora on commercial apple fruit. This risk was found to be negligible, and this document was used by both the U.S. and New Zealand to argue their respective cases against the fire blight import regulations proposed by Australia for U.S. and New Zealand apples. The third party submission states the reasons why Australia’s regulations are not science-based, and so will be useful for the Office of the U.S. Trade Representative during the upcoming WTO Dispute Settlement Body proceedings. This addresses National Program 303, Component 1, Problem statement 1b.

5.Significant Activities that Support Special Target Populations

6.Technology Transfer

Number of Other Technology Transfer2

Review Publications
Roberts, R.G., Sawyer, A.J. 2008. An updated pest risk assessment for spread of erwinia amylovora and fire blight via commercial apple fruit. Crop Protection Journal. 27:362-368.

Roberts, R.G. 2008. Alternaria roseogrisea, a new species from achenes of Helianthus annuus (sunflower). Mycotaxon. 103:21-26.

Roberts, R.G. 2008. Alernaria undulata, a new species from Citrus sinensis. Mycotaxon. 104:29-34.

Last Modified: 9/3/2015
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