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.
3. Progress 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. We developed PCR assays for fungal pathogens of soybean (Colletotrichum spp., Phakopsora pachyrhizi, and Phytophthora sojae) and viruses (soybean latent spherical virus, and tobacco streak virus). We analyzed the soybean leaf and soil microbiomes for the presence of virulence reducing and yield-enhancing organisms, respectively. The incidence of soybean infecting viruses and green stem disorder were monitored in multiple years. Computer models were developed to describe the effects of weather conditions on the spread of soybean rust spores. The interactions between soybean plants with soybean aphids and the fungi that cause sudden death syndrome and charcoal rot disease were studied. Novel viruses that reduced the virulence of soybean fungal pathogens and soybean cyst nematode were identified and characterized. The genetic and pathogenic variability of isolates of the soybean rust fungus, Phakopsora pachyrhizi, was evaluated. The sensitivity of Phakopsora pachyrhizi (soybean rust) isolates to fungicides was evaluated. Virulence diversity of P. pachyrhizi isolates from the southeastern United States and eastern Africa were compared. A reverse genetic system was established for a fungal virus that reduces the virulence of Sclerotinia sclerotiorum. Objective 2: Identify and genetically characterize resistance in cultivated soybean and related annual and perennial species to pathogens/pests of soybean. More than 150 breeding and/or genetic mapping populations from crosses of germplasm accessions differing in responses to economically important soybean pathogens were developed and used to accomplish project objectives. Molecular markers were identified for regions of soybean chromosomes associated with resistance to bean pod mottle virus, brown stem rot, Diaporthe stem canker, Mexican bean beetle, peanut mottle virus, Phytophthora root rot, potato leafhopper, Reniform nematode, soybean aphid, soybean cyst nematode, soybean mosaic virus, soybean looper, soybean rust, sudden death syndrome, and tobacco ringspot virus. Annual and perennial soybean germplasm accessions were evaluated for resistance to multiple insect species, soybean cyst nematode, soybean rust, and Sclerotinia stem rot. Methods were developed and refined to culture soybean pathogens and to evaluate soybean for resistance responses in greenhouse and field inoculations. The organizations of the chromosomes of one of the wild perennial relatives of soybean were compared to those of cultivated soybean.
1. Developed a sensitive, specific and quantitative molecular assay for the soybean root-rot pathogen Phytophthora sojae. Phytophthora sojae, a soil-borne water mold, causes seed rot, pre- and post-emergence damping-off, and sometimes foliar blight in soybean, a major crop in numerous states. Crop losses may approach 100% with susceptible cultivars. Molecular assays can help farmers determine the presence and amount of this damaging organism in their fields, so that they can select soybean varieties resistant to Phytophthora sojae, or deploy other disease control strategies. ARS scientists at Urbana, Illinois, cooperated with University of Illinois researchers to develop a new molecular assay to detect and quantify the genetic material of Phytophthora sojae without inadvertently detecting related or unrelated microbes that might cause different soybean diseases. Using this assay, technicians can rapidly and reliably help farmers determine what organisms threaten their crops. It will also be useful to scientists who are studying this disease, to find improved resistance to the disease, and to evaluate the spread of Phytophthora sojae in the environment.
2. Identified regions on soybean chromosomes associated with disease resistance by directly analyzing biological and molecular data for the USDA Soybean Germplasm Collection. Genetic resistance is a key strategy for soybean disease management, and multiple genes for resistance have been incorporated into commercial cultivars. In past decades, identification of chromosomal regions containing disease resistance genes necessitated the production of specialized plant populations. In contrast, genome-wide association studies allow the use of genetic variation in natural plant populations to identify chromosomal regions associated with disease resistance. ARS scientists at Urbana, Illinois, cooperated with University of Illinois researchers to use genome-wide association studies of disease sensitivity data and deposited into the USDA-ARS, Germplasm Resources Information Network publicly available high-density molecular marker data to identify chromosomal regions associated with resistance to five fungal, two nematode, and three viral diseases. In some cases, the regions identified were close to chromosomal regions previously reported to condition disease resistance. This information is important to scientists interested in managing soybean diseases through host plant resistance.
3. Showed that viruses that reduce the virulence of soybean fungal pathogens disrupt key fungal gene expression pathways. Sclerotinia sclerotiorum is a widely distributed fungal plant pathogen that causes white mold disease, which significantly reduces yields of soybean and other crops each year. Some mycoviruses (viruses that infect fungi) can be beneficial to agriculture in that they reduce the ability of pathogenic fungi to cause disease. ARS scientists at Urbana, Illinois, cooperated with University of Illinois researchers to show that mycovirus infection altered the expression of S. sclerotiorum genes involved in responding to environmental stresses and pathogen infection. These experiments will be useful to scientists studying the mechanisms by which mycoviruses reduce the severity of diseases caused by fungal plant pathogens.
4. Identified regions of soybean chromosomes containing genes for resistance to soybean rust. Soybean rust is a recurring threat to soybean production in the southern United States, where it is managed primarily by the application of fungicides, which increased production costs. Because populations of the soybean rust fungus are genetically and pathogenically diverse, combining multiple soybean rust resistance genes has been proposed as a strategy to enhance the breadth and durability of soybean rust resistance in new cultivars. To generate information needed to implement the strategy, an ARS scientist in Urbana, Illinois and university cooperators genetically mapped soybean rust resistance genes. The analysis identified soybean germplasm lines with different forms of previously described soybean rust resistance genes (Rpp1-Rpp6) and discovered a new rust resistance gene (Rpp7) in another germplasm line. Soybean breeders can now use DNA markers tightly linked to the mapped genes to produce new soybean cultivars harboring multiple soybean rust resistance genes thereby reducing the economic impact of the disease.
5. Characterized pathotype variation among isolates of the soybean rust fungus (Phakopsora pachyrhizi) collected from the southeastern United States and eastern Africa over time. Soybean rust, caused by the fungus Phakopsora pachyrhizi, is a highly destructive disease that causes substantial yield losses in many soybean-producing regions throughout the world. Knowledge about P. pachyrhizi virulence is needed to guide development and deployment of soybean varieties with durable resistance against most rust populations. ARS scientists in Urbana, Illinois and university cooperators assessed the pathotype variation of P. pachyrhizi isolates using 11 soybean lines expressing different soybean rust resistance genes. Considerable pathotype diversity among populations of the fungus between sequential growing seasons was observed; highly virulent pathotypes were present in one growing season, but often did not persist into the next season. Soybean lines carrying four resistance genes were resistant against most of the isolates and therefore may be useful for soybean-breeding programs. These results will be of interest to soybean breeders working in developing durable resistance to soybean rust.
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Ajayi, O.O., Diers, B.W., Lagos-Kutz, D.M., Hill, C.B., Hartman, G.L., Reuter-Carlson, U., Bradley, C. 2016. Differential reactions of soybean isolines with combinations of aphid resistance genes Rag1, Rag2, and Rag3 to four soybean aphid biotypes. Journal of Economic Entomology. 109(3):1431-1437. doi:10.1093/jee/tow033.
Chang, H., Haudenshield, J.S., Bowen, C.R., Hartman, G.L. 2017. Metagenome-wide association study and machine learning prediction of bulk soil microbiome and crop productivity. Frontiers in Microbiology. doi: 10.3389/fmicb.2017.00519.
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Twizeyimana, M., Hartman, G.L. 2017. Sensitivity of Phakopsora pachyrhizi (soybean rust) isolates to fungicides and the reduction of fungal sporulation based on fungicide and timing of application. Plant Disease. 101:121-128. doi.org/10.1094/PDIS-04-16-0552-RE.
Chang, H., Hartman, G.L. 2017. Characterization of insect resistance loci in the USDA soybean germplasm collection using genome-wide association studies. Frontiers in Plant Science. 8:670. doi: 10.3389/fpls.2017.00670.
Haudenshield, J.S., Song, J.Y., Hartman, G.L. 2017. A novel, multiplexed, probe-based quantitative PCR assay for the soybean root- and stem-rot pathogen, Phytophthora sojae, utilizes its transposable element. PLoS One. doi.org/10.1371/journal.pone.0176567.
Hill, C.B., Shaio, D., Fox, C., Hartman, G.L. 2017. Characterization and genetics of multiple soybean aphid biotype resistance in five soybean plant introductions. Theoretical and Applied Genetics. 130:1335–1348.
Murithi, H.M., Haudenshield, J.S., Beed, F., Mahuku, G., Joosten, M., Hartman, G.L. 2017. Virulence diversity of Phakopsora pachyrhizi isolates from East Africa compared to a geographically diverse collection. Plant Disease. 101:1194-1200.
Wen, L., Yuan, C., Herman, T.K., Hartman, G.L. 2017. Accessions of perennial Glycine species with resistance to multiple types of soybean cyst nematode (Heterodera glycines). Plant Disease. 101:1201-1206.