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United States Department of Agriculture

Agricultural Research Service

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Research Project: Systematics and Diagnostics of Emerging and Quarantine-Significant Plant Pathogenic Fungi

Location: Mycology and Nematology Genetic Diversity and Biology Laboratory

2012 Annual Report

1a. Objectives (from AD-416):
1. Identify and describe invasive and emerging plant pathogens, including rust and smut pathogens of quarantine significance; canker and anthracnose pathogens of tree, forage, and oil crops; and fungi associated with potential biofuel crops. 2. Develop robust phylogenetic classification systems for plant-associated fungi to better predict pathogen behavior and to enable development of accurate diagnostic methods for closely related or morphologically similar species.

1b. Approach (from AD-416):
Fungi in these groups will be collected, cultured and characterized microscopically to screen for taxa of interest and provide provisional identifications. For smut and bunt fungi, initial focus will be on species of Tilletia closely related to dwarf bunt, T. controversa. Species of Ustilago including segregate genera and Urocystis (flag smut) will also be collected and characterized as encountered. Species of Phomopsis and related canker pathogens in the Gnomoniaceae will be the major focus among the canker fungi as well as Neonectria and related nectriaceous fungi. Rust and anthracnose fungi (primarily Colletotrichum) associated with sugarcane, switchgrass, and turf grasses will also be collected and characterized. PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, EF1-alpha, and RNA polymerase gene regions. For determining initial identities and superficial relationships of newly obtained taxa, the ITS regions of the nuclear ribosomal repeat unit will be sequenced, compared with existing data in GenBank, and correlated with morphological data. For determining species relationships across these genera and relationships of genera, the ITS, LSU, tef1-a, ß-tub, and rpb gene regions will be analyzed along with other genes to be determined including the single copy DNA lyase Apn2, Mat1M72F/R for the combined Mat1, intergenic region and 5’ Apn2 and the single copy SOD2 gene. Whole genome DNA sequencing from Colletotrichum isolates will be performed using short read next generation sequencing technology from genomic DNA. Population-level and phylogenomic relationships of anthracnose pathogens of grasses will be determined. For population scale analyses, genotypic data will be combined into multilocus haplotypes for each isolate and used to perform population genetic analyses. Coalescent-based analyses may be applied in an interactive manner based on observed population considerations to provide estimates of parameters such as migration, historical population sizes, and test for evolutionary scenarios that reflect various demographic outcomes. As new pathogens in these groups emerge, species previously unknown to science yet related to known pathogens in these groups will be described, illustrated and characterized. Taxonomic monographs will be published and made available as online resources as well as PCR-based diagnostic assays for pathogens of agronomic significance.

3. Progress Report:
This report documents progress for the Project 1275-22000-279-00D, Systematics and Diagnostics of Emerging and Quarantine-Significant Plant Pathogenic Fungi and continues research from Project 1275-22000-245-00D, Systematic Biology of Invasive and Emerging Plant Pathogenic Fungi. This project focuses on National Program 303, Component 1, Plant Diseases, Diagnostics, Etiology and Systematics. Progress was made on both objectives, which fall under Problem Statement 1, Diagnostics, Etiology and Systematics of Plant Disease and use molecular and morphological approaches to classify and characterize taxonomically difficult groups of disease-causing fungi. This enables accurate identifications, which are essential for controlling the diseases these fungi cause, to breed for resistance, and to alleviate potential plant quarantine and import/export issues. Under Objective 1, significant progress was made in developing a diagnostic test to determine the presence of the cause of boxwood blight. Under Objective 2, significant progress was made towards resolving the phylogeny of a group of fungi including several tree pathogens to determine and predict the environmental conditions correlated with host associations and speciation events.

4. Accomplishments

Last Modified: 10/18/2017
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