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United States Department of Agriculture

Agricultural Research Service

Research Project: SYSTEMATIC BIOLOGY OF INVASIVE AND EMERGING PLANT PATHOGENIC FUNGI
2010 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.

Orange rust of sugarcane is new to the United States and losses up to 40% in cane tonnage have now been documented in Florida in susceptible cultivars. Additionally it can cause an overall reduction in sugar purity. Strains of orange rust from the U.S. have been compared with samples from around the world as well as brown rust on sugarcane that is already prevalent in the Americas. This research is continuing in collaboration with USDA-ARS research scientists in Florida.

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. Research is continuing on the wood-inhabiting species with a number of additional taxa have been 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.


4.Accomplishments
1. Orange rust of sugarcane new to U.S. compared worldwide: sugarcane rust fungi not closely related. Rust fungi are a very large and diverse group of parasites that attack crop plants. Accurate knowledge of the relationships among these fungi is important for controlling the diseases they cause. In this research a rust fungus on sugarcane recently introduced into the United States was compared to another rust fungus on sugarcane. Specimens were obtained from throughout the world. Using DNA sequence data it was determined that these two species are not closely related despite the fact that they infect the same host. Knowledge of these plant pathogenic fungi will be used by agronomists and plant pathologists who are working to control the rust fungi on sugarcane.

2. Breeding for resistance to chickpea rust requires screening a wide host range. Chickpea rust is a serious disease that causes considerable damage to this crop each year. Plant breeders are working to develop chickpea varieties that are resistant to the rust fungus but are hindered by lack of knowledge about the identification and host range of the chickpea rust. Until now, this fungus was thought to infect only chickpea and one species of Medicago. Recently the chickpea rust fungus was discovered on a weed called hairy medic suggesting that the host range was much broader than previously known. In this research chickpea rust was determined to infect a wide range of host plants in the legume tribe Trifolieae, specifically 29 species of Medicago including alfalfa and three species of Melilotus. These hosts suggest that other crops and weeds growing near the chickpea fields may serve as a reservoir for this disease-causing fungus. DNA sequences were determined to aid in the identification of this fungus. Plant pathologists and plant breeders will use this research in disease management and for developing chickpea varieties resistant to this disease as well as for more accurate idenfication of rust fungi on these hosts.

3. Telial state of Japanese apple rust on juniper and confirmation of aecial state on domestic apple 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.

4. New smut fungus found on grass seed for trade. Bunt fungi cause serious diseases of grass crops, yet not all species are known even inside the United States. A previously unrecognized species of Tilletia was detected in seeds of alkali grass from Washington. The fungal pathogen was characterized and described as a new species, Tilletia puccinelliae, using morphology and DNA sequences. Recognition of this new species will be important to the seed trade, especially when inspecting grass seeds for import or export.


Review Publications
Minnis, D., Rossman, A.Y., Clement, D., Malinowski, M.K., Rane, K.K. 2010. First report of powdery mildew caused by Podosphaera leucotricha on Callery pear in North America. Plant Disease. 94:279.

Lechat, C., Farr, D.F., Hirooka, Y., Minnis, D., Rossman, A.Y. 2010. A new species of Hydropisphaera, H. bambusicola, is the sexual state of Gliomastix fusigera. Mycotaxon. 111:102.

Yun, H., Minnis, A., Dixon, L.J., Castlebury, L.A. 2010. First report of Uromyces acuminatus on Honckenya peploides, the endangered seabeach sandwort. Plant Disease. 94:279.

Schoch, C., Crous, P., Groenewald, J., Barres, B., Boehm, E., Degruyter, J., De Hoog, G., Dixon, L.J., Fournier, J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, Hirayama, K., Hosoya, T., Hyde, K., Jones, E., Kohlmeyer, J., Lucking, R., Lumbsch, H., Lutzoni, F., Marvanova, L., Mbatchou, J., Miller, A., Mugambi, G., Muggia, L., Nelson, M., Nelson, P., Owensby, C., Phongpaichit, S., Pointing, S., Pujade-Renaud, V., Raja, H., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wood, A., Woudenberg, J., Yonezawa, H., Zhang, Y., Spatafora, J. 2009. A class-wide phylogenetic assessment of Dothideomycetes. Studies in Mycology. 64:1-15.

Kuleci, E., Tunali, B., Berner, D.K., Cavin, C.A., Castlebury, L.A. 2009. First report of leaf anthracnose caused by Phomopsis convolvuli on field bindweed in turkey. Plant Disease. 93:847.

Mengistu, A., Boykin, D.L., Castlebury, L.A., Smith, J.R., Ray, J.D., Bellaloui, N. 2009. Seasonal Progress of Phomopsis longicolla on Soybean Plant Parts and its Relationship to Seed Quality. Plant Disease. 93:408-411.

Hirooka, Y., Kobayashi, T., Ono, T., Rossman, A.Y., Chaverri, P. 2010. Verrucostoma, a new genus in the Bionectriaceae from the Bonin Islands, Japan. Mycologia. 102(2):418-429.

Bruckart, W.L., Eskandari, F., Berner, D.K., Aime, M.C. 2009. Life cycle of Puccinia acroptili. Mycologia. 102(1):62-68.

Dixon, L.J., Castlebury, L.A., Aime, M., Glynn, N.C., Comstock, J.C. 2010. Phylogenetic relationships of sugarcane fungi. Mycological Progress. 9(4):459-468.

Glynn, N.C., Dixon, L.J., Castlebury, L.A., Szabo, L.J., Comstock, J.C. 2010. PCR assays for the sugarcane rust pathogens Puccinia kuehnii and P. melanocephala and detection of a SNP associated with geographic distribution in P. kuehnii. Plant Pathology. 59:703-711.

Flores, C., Loyo, R., Ojeda, A., Rangel, C.A., Ceron, F., Marquez, W., Guerra-Moreno, A.S., Hernandez, H.M., Gonzalez, R.E., Castlebury, L.A., Dixon, L.J., Glynn, N.C., Comstock, J.C., Flynn, J., Amador, J. 2009. First Report of Orange Rust of Sugarcane Caused by Puccinia kuehnii in Mexico, El Salvador and Panama. Plant Dis. 93:1347

Stuteville, D., Graves, W., Dixon, L.J., Castlebury, L.A., Minnis, A. 2010. Uromyces ciceris-arietini, the cause of chickpea rust: new hosts in the Trifolieae, Fabaceae. Plant Disease. 94(3):293-297.

Bao, X., Carris, L.M., Huang, G., Luo, J., Liu, Y., Castlebury, L.A. 2010. Tilletia puccinelliae, a new species of reticulate-spored bunt fungus infecting Puccinellia distans. Mycologia. 102:613-623.

Rossman, A.Y., Farr, D.F., Schoch, C., Nishijima, K.A., Keith, L.M., Goenaga Portela, R.J. 2010. Phylogeny and redescription of Dolabra nepheliae on rambutan and litchi. Mycoscience. 51:300-309.

Last Modified: 11/28/2014
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