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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Research Project #422909


Location: Soybean/maize Germplasm, Pathology, and Genetics Research

2013 Annual Report

Objective 1: Use pathogen/pest virulence and genomics data to develop quantitative detection methodologies that will be used to monitor the spread, diversity, and impact of these biotic agents. Sub-objective 1.A. Characterize soybean pathogens and pests in terms of their aggressiveness, virulence, and molecular and genetic diversity. Sub-objective 1.B. Evaluate the impact of soybean cyst nematode and F. virguliforme on yield when using host resistance genes and plant defense elicitors. Sub-objective 1.C. Develop and utilize molecular markers to monitor soybean pathogens and pests. Objective 2: Identify and genetically characterize resistance in cultivated soybean and related annual and perennial species to pathogens/pests of soybean. Sub-objective 2.A. Identify new sources of pathogen/pest resistance in annual and perennial accessions from the USDA Soybean Germplasm Collection. Sub-objective 2.B. Genetically and phenotypically characterize identified resistance to soybean pathogens and pests. Sub-objective 2.C. Develop improved soybean germplasm and breeding lines that carry disease and pest resistance genes.

The distribution and diversity of soybean pests and pathogens will be monitored using phenotypic evaluations and molecular diagnostic assays developed from pathogen genome sequence data. The impacts on soybean yields of selected pathogens and pests with and without the application of chemical inducers of disease resistance will be characterized in replicated field trials over multiple years using soybean lines that differ in their levels of resistance. Resistance to pathogen and pests will be identified and characterized in cultivated soybean and related annual and perennial accessions from the USDA Soybean Germplasm Collection through field and greenhouse evaluations. Molecular markers for regions of soybean chromosomes associated with pathogen/pest resistance and regions of pathogen chromosomes associated with virulence will be identified by molecular mapping techniques. The information gained during the characterization of soybean germplasm accessions will be used to produce breeding lines with enhanced resistance to pathogens and pests by a combination of breeding and marker assisted selection techniques.

Progress Report
To increase the efficiency and accuracy of diagnosis of soybean anthracnose, real-time multiplex quantitative PCR assays were designed to discriminate Colletotrichum species that cause the disease. Colletotrichum isolates were collected from soybean with anthracnose symptoms in AL, AR, IL, and MS. Based on morphological characteristics and gene sequence analyses, four Colletotrichum species were identified: C. chlorophyti, C. destructivum, C. truncatum, and a new Colletotrichum species (C. maxi). Two assays were designed, were used to characterize more than 100 isolates and proved to be a rapid and accurate method to detect Colletotrichum species. In collaboration with the University of Georgia, a set of 114 plant introductions (PIs) previously evaluated for resistance to soybean rust were retested for rust resistance in the field and greenhouse in GA. Breeding lines derived from crosses of elite soybean lines and exotic PIs with resistance to soybean rust or other disease were evaluated for resistance and agronomic traits in IL or FL. In 2012, ca. 2,500 lines were grown in FL and ca. 1,800 lines were grown in IL and evaluated in the field for disease resistance and/or agronomic traits. Selected lines from FL and IL were reevaluated in 2013. Germplasm accessions with resistance to soil pathogens in northern FL were assayed for resistance to Rhizoctonia in Illinois. To generate molecular resources for gene mapping and identification in Glycine latifolia, a wild perennial relative of soybean, a population of 186 G. latifolia F2 individuals that segregated resistance to white mold was genotyped by high-throughput sequencing. The analysis generated more than 2,000 molecular markers that segregated to form 20 large linkage groups, many of which were syntenic with soybean chromosomes. Molecular marker and phenotypic data were combined to identify chromosomal regions associated with resistance to white mold in G. latifolia. Four replications of a population of 200 diverse soybean lines that differ in the rates at which they transmit Soybean mosaic virus (SMV) through seed were inoculated with SMV in a greenhouse experiment. The plants will be grown to maturity and assayed for rates of SMV seed transmission. For bimolecular fluorescence complementation studies, we cloned genes encoding the coat and resistance suppressor proteins from SMV isolates that are either poorly or efficiently transmitted through seed into appropriate expression plasmids and verified the constructions. In collaboration with a USDA researcher from Stoneville, MS and two scientists from the University of Arkansas, elite Midwestern soybean lines were crossed with 13 germplasm accessions resistant to Phomopsis seed decay (caused primarily by Phomopsis longicolla). Populations from the earliest crosses were advanced. In collaboration with a researcher from The Ohio State University, eight soybean accessions resistant to Phytophthora sojae were crossed to elite Midwestern parents to create breeding lines and to Phytophthora-susceptible parents to produce populations for genetic mapping.

1. Identified molecular markers for gene mapping in a perennial wild relative of soybean. Like many widely cultivated crops, soybean has a relatively narrow genetic base, while its wild relatives are more genetically diverse and display desirable traits, including disease resistance, not present in cultivated soybean. Transferring the genes underlying these valuable traits to soybean from its wild relatives has been hampered by a lack of molecular markers to follow the genes during the arduous process of crossing wild and cultivated plants. Using high-throughput sequencing, ARS scientists at Urbana, IL in collaboration with researchers at the University of Illinois identified more than 9,000 high-quality molecular markers in a wild relative of soybean that show resistance to white mold, an important disease of soybean for which complete resistance is not available in soybean. The identified molecular markers will be useful for gene mapping and the movement of agronomically important genes into soybean. The results will be of interest to scientists who are interested in utilizing the genes from genetically diverse wild soybean species for soybean improvement.

2. Showed that isolates of the soybean rust fungus from the southern U.S. can infect commonly used resistant soybean lines. Soybean rust is a damaging disease of soybean in the southern United States and other tropical and subtropical regions of the world that is caused by the fungus Phakopsora pachyrhizi. Two genes have been effective at protecting soybean plants from damage by domestic rust populations. However, ARS scientists at Urbana, IL in collaboration with researchers at the University of Florida showed that isolates of the soybean rust fungus from Florida caused high levels of disease on plants with either of the two resistance genes. These studies showed the importance of identifying new sources of resistance to soybean rust for sustainable management of the disease. The results will be of interest to scientists who are interested in enhancing the resistance of soybean to soybean rust and studying the dynamic virulence properties of pathogen populations and to soybean growers who need to select cultivars with effective resistance to soybean rust.

3. Developed a rapid and reliable method for detecting viable soybean rust spores. Soybean rust, caused by the fungus Phakopsora pachyrhizi, is a damaging disease of soybean grown in tropical and subtropical regions of the world. The disease was first identified in the Americas in Brazil in 2001 and the continental U.S. in 2004. Early warning systems have been developed for the fungus that capture and count fungal spores in collected rainwater or air-borne spores on sticky traps. These methods for detection have been used to recommend early applications of fungicides, but they do not determine the viability of spores. ARS scientists at Urbana, IL in collaboration with researchers at the University of Illinois developed a method to quantify viable rust spores in collected samples. The method is rapid and reliable with a potential for application in forecasting soybean rust based on the detection of viable spores. This information will be useful to microbiologists, plant pathologists and epidemiologists interested in developing methods to forecast and cost effectively control soybean rust.

Review Publications
Chawla, S., Bowen, C.R., Slaminko, T., Hobbs, H., Hartman, G.L. 2013. A public program to evaluate commercial soybean cultivars. Plant Disease. 97(5):568-578.
Yang, H., Haudenshield, J.S., Hartman, G.L. 2012. First report of Colletotrichum chlorophyti causing soybean anthracnose. Plant Disease. 96:1699.
Hobbs, H.A., Domier, L.L., Nelson, B.D. 2012. First report of Alfalfa mosaic virus and Soybean dwarf virus on soybean in North Dakota. Plant Disease. 96(12):1829.
Chang, S., Hartman, G.L., Singh, R.J., Lambert, K.N., Hobbs, H.A., Domier, L.L. 2013. Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence. Theoretical and Applied Genetics. 126(6):1627-1638.
Grisham, M.P., Hoy, J.W., Haudenshield, J.S., Hartman, G.L. 2013. First report of orange rust caused by Puccinia kuehnii in sugarcane in Louisiana. Plant Disease. 97(3):426.
Radwan, O., Li, M., Calla, B., Li, S., Hartman, G.L., Clough, S.J. 2013. Effects of Fusarium virguliforme phytotoxin on soybean gene expression suggests a multi-dimensional defense approach. Molecular Plant Pathology. 14 (3):293-307.
Vittal, R., Haudenshield, J.S., Hartman, G.L. 2012. A multiplexed immunofluorescence method identifies Phakopsora pachyrhizi urediniospores and determines their viability. Phytopathology. 102:1143-1152.
Zhang, X., Freire, M., Le, M., Hartman, G.L., Upchurch, R.G., Pedley, K.F., Stacey, G. 2012. Genetic diversity and origins of Phakopsora pachyrhizi isolates in the United States. Asian Journal of Plant Pathology. 6:52-65.
Cortina, J.V., Theodoro, G., Walker, D.R. 2013. Identification of fungi on diseased soybean seeds harvested during a high rainfall period in Mato Grosso do Sul, Brazil. Bioscience Journal. 29:386-391.
Nam, M., Bae, H., Hammond, J., Domier, L.L., Youn, Y., Lee, B., Lim, H. 2013. Seed transmission rates of Bean pod mottle virus and Soybean mosaic virus in soybean may be affected by mixed infection or expression of the Kunitz trypsin inhibitor. Research in Plant Disease. 19(2):114-117.
Han, J., Domier, L.L., Dorrance, A., Qu, F. 2012. Complete genome sequence of a novel pararetrovirus isolated from soybean. Journal of Virology. 86(17):9555. DOI:10.1128/JVI.01558-12.
Han, J., Domier, L.L., Dorrance, A., Qu, F. 2013. First report of soybean vein necrosis-associated virus in Ohio soybean fields. Plant Disease. 97(5):693.
Delaney, M.A., Sikora, E.J., Delaney, D.P., Palm, M.E., Haudenshield, J.S., Hartman, G.L. 2012. First report of Soybean Rust (Phakopsora pachyrhizi) on Florida Beggarweed (Desmodium tortuosum) in Alabama. Plant Disease. 96(9):1374.