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United States Department of Agriculture

Agricultural Research Service

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2009 Annual Report

1a. Objectives (from AD-416)
Characterize and analyze phylogenetic relationships for important disease-causing basidiomycetes with emphasis on smut and bunt fungi on cultivated grains and turf grasses, and rust fungi as pathogens of crops. Characterize and analyze phylogenetic relationships of ascomycetous pathogens based on morphological and molecular characteristics with emphasis on canker and related anthracnose fungi causing diseases of tree fruit crops and forest trees.

1b. Approach (from AD-416)
Smut and bunt fungi associated with turf grasses, cultivated grains, and weedy plants in the genera Tilletia, Ustilago, and Urocystis will be collected, cultured and characterized with morphological and molecular data. A wide range of rusts on weedy and crop plant hosts will be collected and characterized with DNA sequence data in order to determine both higher-level relationships and species relationships. Taxon-specific PCR primers will be developed for genes of interest when necessary. For both rusts and smuts PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, SSU, EF1-alpha, and RNA polymerase gene regions. Species concepts will be defined based on multi-gene phylogenetic trees and morphological data when possible. Fungal pathogens of tropical hosts will be characterized with molecular data and ribosomal gene regions will be used to determine their relationships. Sequence data will be used to develop rapid methods for identification and correlated with morphological data when available. Diaporthalean taxa, including Diaporthe-Phomopsis and Valsa-Cytospora and taxa in the Nectria family of the Hypocreales will be collected and characterized morphologically. PCR will be performed to amplify ribosomal and protein-coding genes, including ITS, LSU, SSU, EF1-alpha, and RNA polymerase gene regions. Species concepts will be defined based on multi-gene phylogenetic trees in combination with morphological data. 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.

3. Progress Report
This research uses molecular and morphological approaches to classify and characterize taxonomically difficult groups of disease-causing fungi. Agricultural crops and forest trees are threatened by fungal pathogens that cause over $20 billion damage each year. Rust and bunt fungi are relatively unstudied especially using molecular approaches to understand species-level relationships. Similarly, canker and anthracnose diseases caused by ascomycetes are relatively unknown. As new pathogens in these groups emerge, often they represent species that were previously unknown to science. Characterizing and defining relationships of new and emerging diseases in these groups of plant pathogenic fungi are essential for accurate identification in order to control the diseases these fungi cause, to breed for resistance, and to alleviate potential plant quarantine including import/export issues. The bunt fungi in the genus Tilletia are an important but poorly known group of plant pathogens. Research is continuing in collaboration with a scientist at Washington State University to discover, describe and phylogenetically characterize the bunt fungi on cereal crops in the United States. Research on canker causing fungi has resulted in monographic accounts of several genera as well as a number of newly discovered species. A paper on the leaf-inhabiting genera was published. Research is continuing on the wood-inhabiting species with a number of additional taxa discovered. Research to define the genera within this family has been completed. The new generic concepts are based on a classification determined by the analyses of sequences from several genes. The redefined genera include those species related to the type species. In most cases the traditional definition of the genus based on characters of ascospore septation and stromatal features must be altered. New and subtle morphological characters as well as host plant are used to define these genera. Research on canker-causing fungus in the Hypocreales has progressed with a monographic account of the genus Nectria soon to be submitted for publication. Several new fungal pathogens in the United States have been discovered and reported. Japanese apple rust was discovered for the first time in the mid-Atlantic states. Research on this group of rust fungi is progressing. Also, new parasitic fungi on the biofuel switchgrass and sugarcane were identified and reported.

4. Accomplishments
1. Japanese apple rust discovered in eastern United States. Rust fungi are a large and diverse group of parasites that attack crop and forest plants. Accurate knowledge of the distribution of rusts is important for tracking the movement of these disease-causing fungi. In this research a rust fungus that infects apples and other plants in the same genus was discovered for the first time in the North America. The rust was observed on leaves of crab apple in Delaware and Pennsylvania. Until now, this rust species was known only from Asia. Knowledge of the distribution of plant pathogenic fungi is useful to agronomists and plant pathologists as well as plant regulatory and quarantine officials.

2. Monograph of leaf-blight fungi related to chestnut blight. Fungi are a group of organisms that cause billions of dollars damage to agricultural and forest resources in the United States each year. One group of fungi includes the species that caused chestnut blight in the eastern United States killing all of the chestnut trees. In this research leaf-blight fungi are described and illustrated in a family related to chestnut blight fungi. A key for identification is provided. Relationships between these species were determined based on DNA sequences. Many of these species occur on hardwood trees in North America and cause serious anthracnose diseases. This paper will be used by forest pathologists to determine the fungi that cause diseases on hardwood trees.

3. New parasitic fungi reported on biofuel switchgrass. Switchgrass is a fast-growing plant that is being considered for large-scale production as a source of biofuels. Knowledge of the plant pathogens that cause diseases of this plant is limited. In growing a wide range of switchgrass in Texas and Tennessee, two parasitic diseases were discovered not previously known to those regions. One is a rust fungus to which all cultivars are susceptible. The other is a bunt fungus that completely replaces the host seed tissue. These fungi were sequenced to determine their accurate identification. This research will be used by plant pathologists who are developing strategies to control the disease caused by these parasitic fungi.

Review Publications
Carris, L.M., Castlebury, L.A. 2008. The first report of the Rye Smut, Tilletia secalis, from North America. North American Fungi. 3(7):147-159.

Rossman, A.Y. 2008. The impact of invasive fungi on agricultural ecosystems Biological Invasions. 92:1376-1386.

Thomas, S.E., Crozier, J., Aime, M.C., Evans, H.C., Holmes, K.A. 2008. Molecular characterization of fungal endophytic morphospecies associated with the indigenous forest tree, Theobroma gileri in Ecuador. Mycological Research. 112:852-860.

Freshour, L., Agarwal, S., Sorochan, J., Zale, J., Ownley, B., Gwinn, K., Castlebury, L.A., Carris, L.M. 2008. First report of Puccinia emaculata on switchgrass (Panicum virgatum L.) in Tennessee. Plant Disease. 92:1710.

Yun, H., Minnis, A., Rossman, A.Y. 2009. First report of Gymnosporangium yamadae, Japanese apple rust, on Malus from North America. Plant Disease. 93:430.

Sogonov, M.V., Castlebury, L.A., Rossman, A.Y., Mejia, L.C., White, J.F. 2008. Leaf-inhabiting Genera of the Gnomoniaceae, Diaporthales. Studies in Mycology. 62:1-79.

Carris, L.M., Castlebury, L.A., Zale, J. 2008. First report of Tilletia pulcherrima on switchgrass (Panicum virgatum L.) in Texas. Plant Disease. 92:1707.

Yun, H., Rossman, A.Y., Byrne, J. 2009. First report of Gymnosporangium sabinae, European pear rust, on Bradford pear in Michigan. Plant Disease. 93(8):841.

De Silva, H., Castlebury, L.A., Green, S., Stone, J.K. 2009. The phylogenetic relationship between Anisogramma virgultorum and A. anomala within the Diaporthales (Ascomycota). Mycological Research. 113:73-81.

Cline, E., Rossman, A.Y. 2007. Septoria malagutii sp. nov., cause of annular leaf spot of potato. Mycotaxon. 98:125-135.

Schoch, C., Blackwell, M., Bonito, G., Castlebury, L.A., Crous, P., Geiser, D., Lutzoni, F., O Donnell, K., Rossman, A.Y., Spatafora, J. 2009. The Ascomycota tree of life: A phylum wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology. 58(2):224-239.

Chavarria, E., Subiros, F., Vega, J., Ralda, G., Glynn, N.C., Comstock, J.C., Castlebury, L.A. 2009. First report of Orange Rust of Sugarcane Caused by Puccinia kuehnii in Costa Rica and Nicaragua. Plant Dis. 93:425.

Last Modified: 2/23/2016
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