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United States Department of Agriculture

Agricultural Research Service

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

2010 Annual Report

1a. Objectives (from AD-416)
1: Develop and use quantitative methodologies to detect, identify, and characterize soybean pathogens and monitor the spread of disease epidemics. 2: Identify viral and host determinants of horizontal and vertical transmission of soybean viruses. 3: Identify and improve germplasm with soybean disease resistance using phenotypic and marker-assisted selection. 4: Develop and improve integrated strategies for sustainable disease management in soybean. Sub-objectives: a. Determine the efficacy of fungicides and optimize cultural practices for the management of soybean rust. b. Develop and validate biological control protocols for bacterial agents against soybean cyst nematode.

1b. Approach (from AD-416)
1) Pathogens will be collected from diseased plants, air, soil, and water and phenotypically and molecularly characterized to identify nucleotide sequences that will be used to quantitatively identify pathogenic organisms and to determine genetic variability of pathogens. 2) To identify viral determinants of transmission, transmission phenotypes of chimeric viruses constructed from viruses differing in transmission properties will be evaluated; regions of the soybean genome involved in seed transmission will be identified using molecular markers and populations of soybean plants differing in transmission of virus through seed. 3) Potential sources of soybean resistance genes and populations segregating for resistance will be evaluated in nurseries and other sites appropriate for resistance screening tests. 4) Soybean germplasm accessions with resistance will be crossed with selected cultivars and lines to create populations used for inheritance and mapping studies. Fungicide trials will evaluate fungicide efficacy, sprayer/delivery technology, timing and frequency of applications, possible interactions between fungicides and soybean genotypes, row spacing, irrigation, and plant architecture on soybean rust infection. Molecular techniques will be developed to identify and quantify obligately parasitic, biological control bacteria in soybean cyst nematode populations and in field soil and culture of bacteria will be attempted using proprietary technology.

3. Progress Report
Objective 1: In 2010, we studied the distribution, virulence and diversity of soybean pathogens and developed and utilized quantitative methods for pathogen detection and discrimination. We developed a rapid and reliable technique for the detection of viable Phakopsora pachyrhizi urediniospores by integrating an indirect immunofluorescence assay and direct iodine staining. This technique has been used as a research tool to confirm viability of urediniospores based on various treatments and has the potential to be used as an on-site system for forecasting soybean rust by monitoring the movement of airborne spores during the soybean-growing season. Soybean dwarf virus was detected in soybean in south central Illinois. Objective 2: To assess the roles of virus-encoded proteins involved in transmission of Soybean mosaic virus by aphids and through seed, additional site-specific mutations were introduced into virus genes. Soybean plants were inoculated with mutant and unmodified viruses, and rates of seed transmission are being determined from seed of infected plants. The analysis of populations of soybean plants segregating genes for transmission of Soybean mosaic virus through seed and seed-coat mottling when infected by Soybean mosaic virus were completed and a manuscript describing the work was submitted for publication. The role of virus genes in packaging of Soybean dwarf virus genomes in virus particles was studied using recombinant and mutated viruses. Objective 3: Tobacco streak virus is considered a possible emerging virus disease of soybean in the Midwest. This year, we evaluated over 1000 soybean lines for resistance to Tobacco streak virus and identified nine lines that showed resistance to the virus. We also evaluated the segregation of resistance to Tobacco streak virus in populations of soybean plants derived from crosses between susceptible and resistant soybean lines. Objective 4: Application of fungicides currently is the most effective means of limiting soybean rust disease severity. In FY2010, we examined the differential production and germination of urediniospores of 15 different isolates of the fungus that causes soybean rust, Phakopsora pachyrhizi, following fungicide treatment at different temperatures. Urediniospore production was highest at moderate temperatures and lowest at high temperatures. In addition, Phakopsora pachyrhizi isolates differed significantly in their sensitivity to fungicide treatment. The results showed that temperature plays a significant role in urediniospore production and that diversity exists within Phakopsora pachyrhizi populations for fungicide sensitivity that could lead to selection of fungicide-tolerant fungal populations and reduced efficacy of fungicides currently in use to control soybean rust.

4. Accomplishments
1. Resistance of soybean germplasm to 2009 populations of the soybean rust fungus identified or confirmed. Soybean rust, caused by the fungus Phakopsora pachyrhizi, is an important disease in many soybean-producing countries and was first reported in the continental United States in 2004. Phakopsora pachyrhizi has proven highly adept at overcoming major rust resistance genes and evolving tolerance to fungicides. Identification and utilization of diverse resistance genes for breeding programs is therefore an important component of an integrated strategy for long-term management of soybean rust. ARS researchers at Urbana, Illinois in collaboration with university scientists from Alabama, Florida, Georgia, Louisiana, and South Carolina evaluated the responses of accessions from the USDA Soybean Germplasm Collection to field populations of the rust fungus at five locations and found that most, but not all, accessions that were resistant to soybean rust in previous years were resistant to rust in 2009. In addition, ARS researchers in collaboration with scientists at universities in Iowa, Missouri, North Carolina and Canada detected variation for rust susceptibility in approximately 800 USDA-ARS and 750 public breeding lines, which allowed selection of lines that were resistant to rust and showed no symptoms or indications of infection with viruses or other pathogens. Identification of soybean germplasm with resistance to soybean rust in the United States will facilitate the development of cultivars with broad and durable resistance to this disease.

2. New soybean aphid biotype identified. Shortly after its arrival, the soybean aphid became established as the most important insect pest of soybean in the northern part of the North American soybean production region. Two genes for resistance to soybean aphids (Rag1 and Rag2) have been identified, but a soybean aphid biotype was identified that could colonize soybean plants with the Rag1 resistance gene, which raised concerns about the durability of soybean aphid resistance genes. ARS researchers in collaboration with scientists at the University of Illinois characterized a soybean aphid isolate collected from the overwintering host Frangula alnus in Springfield Fen, IN, and found that the isolate readily colonized plants with the Rag2 resistance gene, distinguishing it from the two biotypes previously characterized. Identification of soybean aphid biotypes that can overcome Rag1 and Rag2 resistance genes suggests that there is high variability in virulence within soybean aphid populations present in North America, which gives the pest a high potential to adapt to and reduce the long-term effectiveness of resistance genes deployed in production. The search for new soybean aphid resistance genes must, therefore, continue, along with the development of alternative sustainable strategies to manage the pest.

3. Identification of regions of soybean chromosomes containing genes that confer resistance to seed transmission of Soybean mosaic virus. Soybean mosaic virus is transmitted through seed and by aphids, and causes one of the most damaging virus diseases of soybean worldwide. In North America, seed-borne infections of Soybean mosaic virus are the primary source of inoculum for disease outbreaks. Hence, reducing seed-borne infections can help reduce the incidence of this virus disease and associated losses in commercial soybean fields. In FY 2010, ARS researchers in Urbana, Illinois in collaboration with scientists from the University of Illinois identified regions on two soybean chromosomes that conferred high levels of resistance to transmission of Soybean mosaic virus through seed. The identification of the chromosomal regions will facilitate the production of soybean cultivars with low levels of transmission of Soybean mosaic virus through seed and lead to a better understanding of the processes that allow Soybean mosaic virus to invade developing soybean embryos.

4. Effects of glyphosate treatment on soybean cyst nematode populations. Soybean cyst nematodes are major yield limiting pests in all major soybean producing countries. In the last decade, soybean cultivars that are tolerant to glyphosate have become widely planted and application of glyphosate to control weeds is now common. ARS researchers at Urbana Illinois evaluated the impact of glyphosate treatment of two soybean cultivars on yield and population development of soybean cyst nematode. In one of the three years examined, they found that glyphosate treatment significantly increased the numbers of soybean cyst nematode eggs associated with one of the two cultivars, but the increase did not result in crop loss. These experiments will be of interest to scientists who are studying the effects of glyphosate use on nontarget microorganisms.

5. Identification of currently available U.S. soybean cultivars with tolerance or partial resistance to soybean rust. Soybean rust is a foliar disease of soybean that can cause very substantial yield losses. However, producing new locally adapted soybean varieties that are resistant or tolerant to soybean rust infections can take years. Tolerant soybean varieties become infected with soybean rust, but have less yield loss than susceptible soybean cultivars. ARS researchers in collaborations with scientists at Auburn University, Clemson University, University of Georgia, and North Carolina State University conducted a two-year study that assessed a group of 12 soybean cultivars for possible tolerance to soybean rust. The least tolerant cultivar, ‘Kuell’, had yield losses as high as 81% in 2009. The most tolerant cultivar, ‘AGS Woodruff’, had yield losses of just 11% in 2008. These data demonstrated that genetic differences in vulnerability to rust-induced yield losses exist among modern soybean cultivars. This information will be of interest to producers who would like to grow high-yielding cultivars that already have at least some resistance or tolerance to soybean rust and will be useful to soybean breeders who wish to incorporate resistance and/or tolerance to soybean rust into their germplasm while minimizing yield drag and other problems often associated with the introduction of resistance genes directly from foreign plant introductions.

6. Demonstration that application of saccharin to plants prior to infection with Phakopsora pachyrhizi can reduce disease severity. A greenhouse experiment conducted in collaboration with University of Florida colleagues at the North Florida Research and Education Center demonstrated that application of saccharin to either soybean roots (as a drench) or to soybean leaves has the potential to significantly reduce soybean rust severity if the plants are subsequently challenged with P. pachyrhizi. While a 0.09 mM saccharin root drench was more effective in reducing disease than a 3 mM foliar application, the latter was also effective when treated plants were inoculated with urediniospores 15 days after the application. Previous research by other groups has shown that saccharin applications can induce systemic acquired resistance in plants, and this is presumably what occurred in the treated soybean plants. Further experiments are needed to determine the value that saccharin applications might have in protecting plants from soybean rust in the field, but the results obtained to date indicate that this might be a viable component of an integrated disease management program.

7. Evaluation of commercial soybean varieties for resistance to Phytophthora root rot and stem rot. Phytophthora sojae causes seed rot, pre- and post-emergence damping-off, and sometimes foliar blight in soybean, and can produce crop losses that approach 100% with susceptible cultivars. The use of resistance has been one of the primary management tools used to control this disease. ARS researchers at Urbana, Illinois in collaboration with scientists from the University of Illinois evaluated Phytophthora root rot resistance among commercial and near-commercial cultivars from private and public soybean breeding programs, and compared these results with the company-provided information on Phytophthora root rot resistance. Single resistance genes were reported in 51% of the entries. This information is useful to soybean scientists in public institutes and private companies that develop soybean cultivars.

8. Influence of environmental conditions on the development of soybean rust epidemics in soybean fields in Nigeria. Soybean rust is a devastating foliar disease of soybean that was first observed in the United States in 2004. Soybean rust is caused by the fungus Phakopsora pachyrhizi and has produced yield losses of up to 80% in experimental trials. To identify environmental factors that favor rust development, ARS researchers in collaboration with scientists at the International Institute of Tropical Agriculture in Ibadan, Nigeria studied soybean rust epidemics in Nigerian soybean fields from 2004 to 2006. Little or late infection was observed on soybeans planted during the dry season (November to March), while disease severity was high and rate of progress was much faster on soybeans planted during the wet season (April to October). Across years, disease severity was consistently higher on soybeans planted in August. Based on these studies, a recommendation was developed suggesting that soybean growers in Nigeria modify their planting date slightly to reduce losses caused by soybean rust.

Review Publications
Goradia, L., Hartman, G.L., Daniel, S. 2009. Evaluation of Glyphosate-Resistant Soybean Cultivars for Resistance to Bacterial Pustule. European Journal of Plant Pathology. 124:331-335.

Slaminko, T., Bowen, C.R., Hartman, G.L. 2010. Multi-Year Evaluation of Commercial Soybean Cultivars for Resistance to Phytophthora sojae. Plant Disease. 94:368-371.

Bradley, C., Hines, R., Haudenshield, J.S., Hartman, G.L. 2010. First Report of Soybean Rust, Caused by Phakopsora pachyrhizi, on Kudzu (Pueraria montana var. lobata) in Illinois. Plant Disease. 94:477.

Hill, C.B., Crull, L., Herman, T., Voegtlin, D.J., Hartman, G.L. 2010. A New Soybean Aphid (Hemiptera: Aphididae) Biotype Identified. Journal of Economic Entomology. 103:509-515.

Paul, C., Hartman, G.L. 2009. Sources of Soybean Rust Resistance Challenged with Six Purified Phakopsora Pachyrhizi Isolates Collected from the USA. Crop Science. 49:1781-1785.

Soria-Guerra, R., Rosales-Mendoza, S., Chang, S., Haudenshield, J.S., Padmanaban, A., Rodriguez-Zas, S., Hartman, G.L., Ghabrial, S., Korban, S.S. 2010. Global Gene Expression Profiles of Resistant and Susceptible Genotypes of Glycine tomentella During Phakopsora pachyrhizi Infection. The Plant Genome. 120:1315-1333.

Kim, K.S., Bellendir, S., Hudson, K. A., Hill, C.B., Hartman, G.L., Hyten, D., Hudson, M.E., Diers, B.W. 2010. Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theoretical and Applied Genetics. 20(5):1063-1071.

Pham, T.A., Hill, C.B., Miles, M., Nguyen, B.T., Vu, T.T., Vuong, T.D., Vantoai, T.T., Nguyen, H.T., Hartman, G.L. 2010. Evaluation of Soybean Germplasm for Resistance to Soybean Rust in Vietnam. Field Crops Research. 117(2010):131-138.

Li, S., Moon, J.S., Lee, S.H., Domier, L.L. 2009. First Report of Soybean Yellow Mottle Mosaic Virus in Soybean in North America. Plant Disease. 93 (11):1214.

Lygin, A., Li, S., Vittal, R., Hartman, G.L., Widholm, J., Lozovaya, V. 2009. The Importance of Phenolic Metabolism to Limit the Growth of Phakopsora pachyrhizi. Phytopathology. 99:1412-1420.

Last Modified: 2/23/2016
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