2012 Annual Report
1a.Objectives (from AD-416):
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.
1b.Approach (from AD-416):
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.
Isolates of the pathogen that causes Pythium root rot were isolated, identified, and evaluated. Twenty-seven species of Pythium were identified, 14 species were not previously reported as pathogens of soybean, and five species were moderately to highly pathogenic on soybean seedlings. Using sequence-based detection techniques a new soybean-infecting pararetrovirus was discovered in collaboration with researchers at The Ohio State University. In collaboration with researchers at the University of Illinois, seven new viruses of fungal pathogens of soybean were identified and QPCR detection methods were developed for each virus.
Through collaboration with colleagues at the University of Georgia, 121 germplasm accessions and susceptible check cultivars were assayed for resistance to soybean rust in a greenhouse in early 2012. The germplasm accessions had been historically resistant to field populations of the rust fungus in the Southeast, or were known to carry previously reported rust resistance genes. Eleven of the germplasm accessions developed susceptible reactions, but the remainder either appeared to be immune or developed the reddish-brown lesions associated with resistance when rated two weeks after inoculation. These results provide guidance for deciding which sources of rust resistance to use in breeding programs and to combine in order to obtain broad and durable resistance to U.S. populations of the rust fungus.
More than 2,500 breeding lines developed by ARS researchers in Urbana, Illinois were planted in the field in Urbana or Quincy, Florida, to be evaluated for agronomic traits and resistance to diseases such as soybean rust, bacterial pustule, Phomopsis seed decay, and virus symptoms. Agronomically superior lines with apparent disease resistance will be selected for further evaluation and confirmation of disease resistance.
Two flavonoids with antimicrobial properties, apigenin and genistein, were evaluated for their abilities to restrict the growth of seven soybean pathogens in amended culture media. Both compounds differentially restricted growth of all seven pathogens. The results suggest that increasing levels of apigenin and genistein may enhance disease resistance in soybean to fungal and oomycete pathogens.
Charcoal rot of soybean is caused by a fungal pathogen and is the leading soilborne disease in many states, but effective resistance to the disease is not available. To develop reliable methods for resistance identification, a cut-stem inoculation technique was evaluated, and was shown to distinguish differences in aggressiveness among isolates of the charcoal rot fungus and relative differences among soybean genotypes for resistance to the charcoal rot fungus.
The coding regions of homologues of DCL3 and RDR6 from soybean accessions either resistant or susceptible to transmission of Soybean mosaic virus (SMV) through seed and the P1-HC-Pro coding regions of SMV isolates either efficiently or poorly transmitted through seed were cloned into BiFC vectors for interactions studies. Experiments were initiated to confirm the in planta expression of the intact fusion proteins.
Identified and characterized viruses infecting soybean fungal pathogens. Sudden death syndrome and Sclerotinia stem rot are two damaging diseases of soybean for which high levels of resistance have not yet been identified in soybean. To identify methods, which might enhance current cultural and chemical control practices for the two diseases, ARS scientists at Urbana, Illinois, along with researchers from the University of Illinois identified six novel RNA viruses infecting isolates of the fungus that causes soybean sudden death syndrome (Fusarium virguliforme) and one virus infecting the fungus that causes Sclerotinia stem rot (Sclerotinia sclerotiorum). Two of the viruses infecting Fusarium virguliforme were associated with significant reductions in the aggressiveness of the virus-infected fungal isolates. Hence, these viruses have the potential to act as biological fungicides that reduce the severity of sudden death syndrome disease symptoms and associated yields losses in soybean.
Characterized the response of soybean fungal and oomycete pathogens to two flavonoids. Soybean plants are constantly under attack in the field by multiple pathogens and pests. To prevent invasion or colonization of plant cells by pathogens, soybean plants recognize invading pathogens and synthesize defense compounds such as flavonoids, some of which have broad spectrum antimicrobial activities. ARS researchers at Urbana, Illinois, in collaboration with scientists from the University of Illinois, tested two flavonoids, apigenin and genistein, for their abilities to alter the growth of seven soybean fungal and oomycete pathogens in amended culture media. Both compounds restricted growth of all seven pathogens, but not all equally. Also, increased concentrations of either compound significantly decreased growth of the pathogens. The results suggest that soybean plants could be made more resistant to fungal and oomycete pathogens if the production of apigenin and genistein could be enhanced through metabolic engineering. This information could be useful to soybean biotechnologists and pathologists that are interested in biological strategies to reduce disease-induced crop losses.
Characterized species that cause Pythium root rot from soil samples. Pythium root rot is a major soybean disease that occurs shortly before or after germinating seedlings emerge from the soil. The disease is caused by water molds from the genus Pythium. Many different species of Pythium have been reported growing in association with soybean and other crops, although not all species are pathogenic on all crops. To evaluate the pathogenicity on soybean seedlings of Pythium species present in Illinois soybean fields, ARS scientists at Urbana, Illinois, in collaboration with researchers from the University of Illinois, obtained, identified, and evaluated the pathogenicity of Pythium species in field soil samples from across Illinois. Twenty-seven species of Pythium were identified, 14 species were not previously reported as pathogens of soybean, and five species were moderately to highly pathogenic on soybean seedlings. This information is important to plant pathologists, soil microbiologists, and other scientists interested in diversity of soilborne pathogens.
Developed evaluation techniques for resistance to charcoal rot in soybean. Charcoal rot of soybean is caused by a fungal pathogen that is the leading soilborne disease in many states, and is especially destructive under dry soil conditions. Effective and reliable methods to evaluate soybean for resistance to this fungus are needed as part of a management scheme that would utilize host resistance. ARS scientists at Urbana, Illinois and researchers from the University of Illinois investigated a cut-stem inoculation technique to evaluate soybean genotypes for resistance to this fungal pathogen. The cut-stem inoculation technique distinguished differences in aggressiveness among isolates of the charcoal rot fungus and differences among soybean genotypes for resistance to the charcoal rot fungus, which were comparable to results from field tests. This information will be useful for soybean breeders, pathologists, and those interested in crop improvement because it provides information on how to evaluate soybean germplasm accessions for resistance to a disease for which there are no resistant soybean cultivars available for growers.
Identified soybean lines resistant to Tobacco streak virus. Tobacco streak virus (TSV) is a damaging pathogen that has been reported in soybean in Brazil and the United States, for which resistance is not currently available in commercial soybean lines. To find additional resistant soybean genotypes, scientists from the University of Illinois and ARS researchers at Urbana, Illinois, evaluated over 1000 soybean accessions from the USDA Soybean Germplasm Collection for resistance to TSV and identified 19 that were resistant to TSV infection. Further investigation showed that the resistant plants showed no symptoms at moderate temperatures, but very severe symptoms at high temperatures when inoculated with TSV. The observations may, at least in part, explain the very severe symptoms observed in TSV-infected plants in Brazil compared to the more mild symptoms often observed in the U.S. This information is important to soybean breeders, plant pathologists, and plant virologists in both private and public sectors that are interested in virus resistance in soybean.
Hobbs, H.A., Jossey, S., Wang, Y., Hartman, G.L., Domier, L.L. 2012. Diverse soybean accessions identified with temperature-sensitive resistance to Tobacco streak virus. Crop Science. 52:738-744.
Jiang, Y., Haudenshield, J.S., Hartman, G.L. 2012. Characterization of Pythium spp. collected from corn and soybean soil in Illinois. Canadian Journal of Plant Pathology. 34(3):448-454. DOI: 10.1080/07060661.2012.705326.
Jiang, Y., Haudenshield, J.S., Hartman, G.L. 2012. Response of soybean fungal and oomycete pathogens to apigenin and genistein. Mycology: An International Journal of Fungal Biology. 3:153-157.
McClellan, M.S., Domier, L.L., Bailey, R.C. 2012. Label-free virus detection using silicon photonic microring resonators. Biosensors and Bioelectronics. 31:338-392.
Twizeyimana, M., Hill, C.B., Pawlowski, M., Paul, C., Hartman, G.L. 2012. A cut-stem inoculation technique to evaluate soybean for resistance to Macrophomina phaseolina. Plant Disease. 96:1210-1215.