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United States Department of Agriculture

Agricultural Research Service

2011 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.

3.Progress Report
This is the final report for the project 5350-22000-016-00D to be terminated in October of 2011. With retirement of the project SY at the end of FY11, ONP decided to terminate the project one year short of its scheduled completion date due to research unit funding limitations. The funding was transferred to project 5350-22000-017-00D, entitled, "Biologically-Based Systems for Soilborned Disease Control in Tree Fruit Agro-Ecosystems".

Activities for this project addressed 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 described research efforts within the project. 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. Over the life of this project, ARS scientists characterized small pieces of DNA that can be used for genealogical analysis that are specific for certain species of exotic mold pathogens. One such piece of DNA is for a gene family known as “aegerolysin”. The entire sequence of this gene from Alternaria gaisen, an exotic pathogen, was obtained and used to design sequencing primers that were successfully used to obtain the aegerolysin sequence from a wide range of species that are pathogenic on various fruits and vegetables around the world. Although some countries want to circumvent these quarantine restrictions by grouping all of these pathogens into an ill-defined “collective” species under the name A. alternata, by comparing the aegerolysin sequences among sets of closely related pathogens, including A. yaliinficiens, A. gaisen, A. longipes, A. alternata, A. mali and a number of citrus pathogens, we found a level of resolution and segregation previously unreported for these pathogens and, therefore, provided molecular data that support maintaining these pathogens as unique species. As many of these pathogens are officially regulated by USDA-APHIS, this information would justify the continued development of DNA-based tests to identify these hitchhiking pathogens so they can be excluded from the USA.

Last Modified: 6/2/2015
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