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United States Department of Agriculture

Agricultural Research Service

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

2007 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
Full-length infectious clones of clover and soybean isolates of SbDV and an SMV isolate with high seed transmissibility were constructed. Strategies were evaluated for infecting plants with infectious clones of SbDV including particle bombardment, agroinfiltration, and embryo wounding. Agroinfiltration was the most successful inoculation technique and produced localized infection in Nicotiana benthamiana, but not in soybean. Seed transmission phenotypes of the SMV full-length clones were verified following mechanical inoculation of plants with in vitro transcripts. The first repetition of experiments for quantitative trait loci (QTL) mapping of genes for resistance to seed transmission was completed. RI populations were advanced and planted in the field for a second repetition of the QTL studies. Progress has been made to develop and use quantitative methodologies to detect, identify, and characterize soybean pathogens and monitor the spread of disease epidemics with the primary focus on soybean rust with emphasis on monitoring, collecting, purifying domestic isolates, and initial development of improved detection assays. Progress also has been made to identify and improve germplasm with soybean disease resistance genes using phenotypic and marker-assisted selection by obtaining materials (plants and pathogens) to screen for new sources of resistance, including testing of segregating materials from cooperators for rust. Advancement of soybean populations already developed for disease resistance was continued, including populations for SDS, rust, and aphid resistance. Additional crosses were made between high-yielding US soybean varieties and foreign (mostly Asian) lines or PIs that have some level of resistance to soybean rust present in the US. Data on the reaction of several hundred PIs to soybean rust were obtained from multiple locations and were provided to the scientific community. Breeding populations from crosses made to 17 rust-resistant germplasm accessions in 2006 are being advanced in the summer of 2007 after being advanced during the winter in Puerto Rico. In early 2007, elite lines were successfully crossed to an additional 16 Asian soybean lines that are believed resistant to rust. Experiments on fungicide efficacy, spray technology, application timing, and fungicide treatment x plant genotype interactions for soybean rust were established. Two fungicide experiments conducted in Urbana, IL and Quincy, FL in 2006 are being repeated in 2007 The ITS region of Heterodera glycines was cloned and sequenced from 24 populations from Asia, North America and South America and is highly polymorphic among and within populations and within some individuals. The HSP90 gene of H. glycines was shown to be polymorphic in populations from Asia, North America, and South America. Specific primers and probes were developed to amplify Pasteuria nishizawae for real-time QPCR.

4. Accomplishments
Mapping locations of soybean aphid resistance genes. The soybean aphid was first identified as a new soybean pest in the U.S. in 2000. Insecticide treatment costs an estimated $84 to $105 million in 2003 to control soybean aphids. Integrating host plant resistance into a pest management system is an economical way to control aphids. Aphid-resistant soybean genotypes have been reported. The objectives of this study were to map the aphid resistance genes in Dowling and Jackson and to identify flanking markers that could be used in marker-assisted selection. Segregation of aphid resistance and simple sequence repeat markers in F2:3 populations developed from crosses between Dowling and the two susceptible soybean cultivars Loda and Williams 82, and between Jackson and Loda, were analyzed. The molecular markers flanking these resistance genes are being used in marker-assisted selection for aphid resistance in soybean breeding programs. This study will be useful for soybean breeders to develop cultivars more rapidly with aphid resistance. (NP# 301 Plant Genetic Resources, Genomics and Genetic Improvement; Research Component -Genomic Characterization and Genetic Improvement) Genetic diversity of the ITS region of the soybean cyst nematode, Heterodera glycines. The ITS region of Heterodera glycines was cloned and sequenced from 24 populations from Asia, North America and South America. The amount of diversity was large, far exceeding any known organism. In some cases several haplotypes were found within the same individual. The amount of diversity among individuals within the same population and among different populations were even greater. These results indicate that concerted evolution is either absent or inefficient for the ITS rDNA gene of the soybean cyst nematode. Concerted evolution would be expected to homogenize the different copies of repeating genes within the genome. Although the ITS gene is not a parasitism gene, these results indicated that the nematode has great diversity and may explain why field populations have great ability to defeat resistance genes of the soybean. (NP #303 Plant Diseases; Research Component – Pathogen Biology, Genetics, Population Dynamics, Spread, and Relationship with Hosts and Vectors) Polymorphism of the Hsp90 Gene among Populations of Heterodera glycines. Hsp90 is a member of a gene family that codes for proteins whose synthesis is enhanced by a variety of environmental stressors, including a sudden increase in temperature. These proteins function as molecular chaperones in cells where they interact with a range of regulatory proteins involved in critical physiological processes such as cell cycle control and hormone signaling. The complete genomic sequence of Hg-hsp90 was done and found to be 3,052-nt long and contained 11 introns, compared with only 3 in Caenorhabditis elegans. The extent of polymorphism of this gene among 16 populations of H. glycines from China (5), Japan (5), and the U.S. (6) was determined. The estimates of gene diversity among populations from China (0.64%), Japan (0.65%), and the U.S. (0.61%) were not significantly different. The extent of variation observed in this study is similar to that obtained with the ITS-rRNA gene, which shows that Hg-hsp90, a single or low copy number gene, unlike the multi-copy ITS-rRNA gene, is a better candidate for nematode phylogenetics. (NP #303 Plant Diseases; Research Component – Pathogen Biology, Genetics, Population Dynamics, Spread, and Relationship with Hosts and Vectors) Interactions between the soybean cyst nematode and the fungal pathogen causing sudden death syndrome. Both soybean cyst nematode and the pathogen causing sudden death syndrome (Fusarium solani f. sp. glycines) are major pathogens of soybean and can cause significant yield losses. Both pathogens are soilborne and infect soybean roots. Studies on the relationship between H. glycines and F. solani f. sp. glycines have been investigated for nearly two decades, but the interaction is not clearly understood. Greenhouse experiments were used to study the interactions between H. glycines and F. solani f. sp. glycines with different inoculum levels of both organisms on a soybean cultivar susceptible to both pathogens. Both H. glycines and F. solani f. sp. glycines affected the growth of soybeans in an additive pattern. Reproduction of H. glycines was suppressed by high inoculum levels of F. solani f. sp. glycines, whereas the low level had no significant impact. Molecular assays were used to quantify fungal infection of soybean roots by F. solani f. sp. glycines and indicated that the infection of soybean roots by H. glycines did not impact colonization of F. solani f. sp. glycines. This study is important to pathologist/nematologists that study interactions of pathogens. (NP #303 Plant Diseases; Research Component – Pathogen Biology, Genetics, Population Dynamics, Spread, and Relationship with Hosts and Vectors) Field evaluation of green stem disorder in soybean cultivars. Green stem is a disorder of soybean that causes the stems to remain green and moist, although pods and seeds are fully mature and dry. The disorder is a nuisance for producers because it complicates harvesting of soybeans by significantly increasing the difficulty in cutting and threshing the affected plants. Over 1,000 soybean cultivars were evaluated for green stem incidence in three Illinois locations, Dekalb, Monmouth, and Urbana, during 2001-2004. There were significant differences among cultivars in 29 of the 31 tests. Consistent differences among cultivars tested in multiple locations and years were found, indicating that genetic variability among cultivars for green stem resistance exists. This study may help growers in selecting cultivars that have less green stem and will provide the basis for additional genetic studies on the inheritance of this trait in soybean so that non-green stem cultivars can be developed. (NP #303 Plant Diseases; Research Component – Host Plant Resistance to Disease) Discovery of soybean rust caused by Phakopsora pachyrhizi on soybean in Illinois. Soybean rust, first reported in the continental United States in Louisiana in 2004, is the most important foliar disease of soybean, worldwide. This disease had not been discovered in Illinois. Extra effort was spent on a survey for the disease late in the season providing the first find of the fungus, causing soybean rust, infecting plants in Illinois. This information provides data on the movement of the soybean rust pathogen that feeds into the national soybean rust modeling and forecasting efforts. (NP #303 Plant Diseases; Research Component – Pathogen Biology, Genetics, Population Dynamics, Spread, and Relationship with Hosts and Vectors)

4. Accomplishments

5. Significant Activities that Support Special Target Populations

Review Publications
Farias Neto, A.F., Hartman, G.L., Pedersen, W.L., Li, S., Bollero, G.A., Diers, B.W. 2006. Irrigation and Inoculation Treatments that Increase the Severity of Soybean Sudden Death Syndrome in the Field. Crop Science 46:2547-2554.

Hartman, G.L., Hines, R.A., Faulkner, C.D., Lynch, T.D., Pataky, N. 2007. Late Season Occurrence of Soybean Rust Caused by Phakopsora pachyrhizi on Soybean in Illinois. Plant Disease. 91(4):466-466.

Li, Y., Hill, C.B., Carlson, S.R., Diers, B.W., Hartman, G.L. 2007. Soybean aphid resistance genes in the soybean cultivars Dowling and Jackson map to linkage group M. Molecular Breeding 19(1):25-34.

Melakeberhan, H., Noel, G.R. 2006. Effects of biosolid soil amendment on Heterodera glycines populations. Journal of Nematology. 38(3):349-353.

Last Modified: 2/23/2016
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