Location: Soybean/maize Germplasm, Pathology, and Genetics Research
2018 Annual Report
Objectives
Objective 1. Relate the spatial and temporal dynamics of soybean pathogens, pests, and associated microbial communities to soybean productivity. Subobjective 1.A. Determine if novel virulent or resistance-breaking soybean pathogens/pests have emerged within the U.S. and other parts of the world. Subobjective 1.B. Determine the impact of selected biocontrol and beneficial microbes to reduce the impact of soybean pathogens and pests. Subobjective 1.C. Characterize variability and shifts in the pathogenicity of Phakopsora pachyrhizi populations in the southern U.S. to guide breeding program decisions.
Objective 2: Identify, characterize, and develop improved resistance in soybean that can be used for sustainable disease management strategies that include effective host resistance and biological control. Subobjective 2.A. Identify or characterize pathogen/pest resistance using annual and perennial accessions from the USDA Soybean Germplasm Collection and selected breeding lines. Subobjective 2.B. Develop agronomically competitive soybean breeding lines with disease- or pest-resistance genes from adapted or unadapted germplasm accessions in the USDA Soybean Germplasm Collection. Subobjective 2.C. Investigate relationships between soybean yields and resistance to soybean cyst nematode and Phytophthora sojae in public breeding lines from the Northern Uniform/Preliminary Soybean Tests.
Approach
The distribution and abundance of soybean pathogens and pests will be monitored on multiple geographic scales using pathogen-specific and metagenomic assays. The impacts of beneficial and insect-borne microbes on soybean diseases and yields will be characterized in replicated trials over multiple years. Changes in pathogen virulence over time will be assessed using soybean lines expressing different pathogen resistance genes and pathogen populations collected from soybean fields each year. New sources of resistance to pathogens 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. Regions of soybean chromosomes associated with pathogen/pest resistance will be identified using phenotypic assays and molecular marker analyses of derived mapping populations. Soybean lines shown to be resistant to soybean pathogens/pests will be used to produce breeding lines with enhanced resistance using phenotypic and marker-assisted selection techniques as appropriate.
Progress Report
For Objective 1 (Relate the spatial and temporal dynamics of soybean pathogens, pests, and associated microbial communities to soybean productivity): Myrothecium leaf spot caused by Paramyrothecium roridum was discovered in Africa for the first time. Morphological and molecular work were completed to verify the pathogen was P. roridum. This is the first confirmed report of P. roridum causing leaf spot on soybean in Africa. The distribution of the pathogen on soybean in the U.S. is not known. Collections of pests from suction traps designed to monitor the soybean aphid occurrence, discovered new distributions for several aphids including the sugarcane aphid and two aphids found on industrial hemp. Identified and characterized a new virus infecting soybean and sugar beet cyst nematodes that has the potential to be used as a biological control agent.
For Objective 2 (Identify, characterize, and develop improved resistance in soybean that can be used for sustainable disease management strategies that include effective host resistance and biological control): Soybean cyst nematode is one of the most important root pathogens of soybean and was recently identified as a potential problem on common bean. Found a significant association between molecular markers in the common bean genome to soybean cysts counts on 363 common bean accessions. Some of the molecular markers were associated with a gene cluster homologous to the three genes at the Rhg1 locus in soybean. The identification of molecular markers in common bean associated with soybean cyst nematode resistance will help to understand the genetic architecture in common bean and how it relates to resistance in soybean. A seventh unique locus with a gene for soybean rust resistance (Rpp7) was identified and mapped in soybean plant introduction (PI) 605823.
Accomplishments
1. Characterized resistance to soybean sudden death syndrome in soybean germplasm lines. Sudden death syndrome (SDS) of soybean is a disease that causes yield losses in soybean growing regions across the USA and worldwide. Soybean resistance to this disease is not a single gene but is controlled by several genes each providing a minor (quantitative) contribution to resistance. The objectives were to incorporate SDS quantitative resistance into elite breeding soybean lines and to integrate consistent SDS resistance nomenclature into the annotation of the soybean genome. ARS researchers at Urbana, Illinois, cooperated with University of Illinois, Iowa State University, Michigan State University, and Southern Illinois University scientists to identify ten chromosomal regions that confer resistance to SDS, which provided a high level of confidence in molecular mapping genes for SDS resistance. In addition, several of the identified soybean lines were used to enhance SDS resistance in elite breeding lines. The information and materials produced here will aid breeders in making decisions to improve resistance to SDS. This information is important to scientists and producers interested in research on managing soybean diseases through host plant resistance.
2. Assembled a draft genome sequence for Glycine latifolia, a wild perennial relative of soybean. Like most cultivated crops, soybean has a relatively narrow genetic base, while its wild perennial relatives are more genetically diverse and can display desirable traits not present in cultivated soybean. For example, no sources of complete resistance to Sclerotinia stem rot have been identified in soybean. However, high levels of resistance have been observed in some accessions of Glycine latifolia. In addition, accessions of G. latifolia show resistance to drought, alfalfa mosaic virus, soybean rust and sudden death syndrome. To identify genes that condition these agronomically valuable traits, ARS researchers at Urbana, Illinois, cooperated with University of Illinois researchers to assemble and annotate the genome sequence of an accession of G. latifolia. The annotation of the G. latifolia genome identified 54,475 high-confidence protein-coding loci, about 1% of which were predicted to be involved in disease resistance or responses to biotic and abiotic stresses. The whole genome sequence and annotation of G. latifolia provides a valuable source of genetic variation that is lacking in soybean germplasm. The results will be of interest to scientists who are interested in utilizing the genes from genetically diverse wild soybean species for soybean improvement.
3. Identified and mapped the location of a novel gene for resistance to soybean rust. Soybean rust (caused by the fungus Phakopsora pachyrhizi) reduces soybean yields and/or increases production costs for soybean growers. Currently, the disease is managed primarily through fungicide applications, which adds additional costs for soybean producers. Planting rust-resistant cultivars would reduce input costs and allow more integrated and sustainable management strategies to be used. Soybean cultivars with two or more rust resistance genes likely would have broader and more durable resistance than soybean cultivars with single rust resistance genes. ARS researchers at Urbana, Illinois, and Frederick, Maryland, cooperated with researchers from the University of Georgia to show that plant introduction 605823, which is resistant to U.S. populations of the rust fungus, possessed a novel rust resistance gene (Rpp7) on soybean chromosome 19. The discovery and mapping of Rpp7 increases the number of genes for resistance to soybean rust that could be combined in new cultivars to reduce fungicide use and to protect soybean yields in production areas of the United States where soybean rust is common.
4. Modelled short-distance aerial movement of soybean rust spores using machine learning. Dispersal of fungal spores by wind is the primary means of spread for the fungus causing soybean rust. In this research, ARS researchers at Urbana, Illinois, cooperated with a University of Illinois scientist to predict short distance movement of soybean rust spores from within the soybean canopy and up to 61 m from field-grown rust-infected soybean plants. Environmental variables were used to develop and compare models to describe deposition of spores collected in passive and active traps. These four models all identified five parameters, distance of trap from source, humidity, temperature, wind direction, and wind speed, as the most important variables influencing short-distance movement of spores. Overall, we found that using multiple machine learning techniques identified the most important variables to make the most accurate predictions of movement of spores found a short distance from the source. This information is important to soybean growers concerned about the movement of spores from surrounding fields and to scientists studying the epidemiology of plant diseases and others interested in the biology of aerial movement of microbes.
Review Publications
Chang, H., Roth, M.G., Wang, D., Cianzio, S.R., Lightfoot, D.A., Hartman, G.L., Chilvers, M.L. 2018. Integration of sudden death syndrome resistance loci in the soybean genome. Theoretical and Applied Genetics. 131:757-773.
Lagos-Kutz, D.M., Halbert, S., Voegtlin, D., Hartman, G.L. 2018. Revision of the taxonomic status of Aphis floridanae Tissot (Hemiptera:Aphididae) using morphological and molecular insight. Insecta Mundi. 0627:1-10.
Godoy, C., Koga, L., Neves De Oliveira, M., Hill, C.B., Hartman, G.L. 2017. Mycelial growth, pathogenicity, aggressiveness and apothecial development of Sclerotinia sclerotiorum isolates from Brazil and the United States in contrasting temperature regimes. Summa Phytopathologica. 43(4):263-268.
Brzostowski, L.F., Pruski, T.I., Hartman, G.L., Bond, J.P., Wang, D., Cianzio, S.R., Diers, B.W. 2018. Field evaluation of three sources of genetic resistance to sudden death syndrome of soybean. Theoretical and Applied Genetics. 131(7):1541-1552. doi.org/10.1007/s00122-018-3096-4.
Romero Luna, M., Mueller, D., Mengistu, A., Singh, A.K., Hartman, G.L., Alane, K. 2017. Advancing our understanding of charcoal rot in soybeans. Journal of Integrated Pest Management. 8(1):1-8. doi:10.1093/jipm/pmw020.
Wen, L., Marzano, S., Ortiz-Ribbing, L., Gruver, J., Hartman, G.L., Eastburn, D. 2017. Suppression of soilborne diseases of soybean with cover crops. Plant Disease. 101:1918-1928.
Wen, L., Bowen, C.R., Hartman, G.L. 2017. Prediction of short-distance aerial movement of Phakopsora pachyrhizi urediniospores using machine learning. Phytopathology. 107:1187-1198.
Hajimorad, M.R., Domier, L.L., Tolin, S.A., Whitham, S.A., Saghai Maroof, M.A. 2018. Soybean mosaic virus: A successful potyvirus with a wide distribution but restricted natural host range. Molecular Plant Pathology. 19:1563-1579.
Yao, X., Han, J., Domier, L.L., Qu, G., Lewis Ivey, M.L. 2018. First report of tomato ringspot virus in an Ohio vineyard. Plant Disease. 102(1):259.
Liu, Q., Chang, S., Hartman, G.L., Domier, L.L. 2018. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. Plant Journal. 91:71-85.
Lagos-Kutz, D.M., Voegtlin, D.J., Hartman, G.L. 2017. Identification of a new species of Aphis (Hemiptera: Aphididae) based on distinct morphology. Insecta Mundi. 0535:1-11.
Vuong, T.D., Walker, D.R. 2018. Advances in marker-assisted breeding of soybean. In: Nguyen, H.T., editor. Achieving Sustainable Cultivation of Soybeans Volume 1: Breeding and cultivation techniques. Cambridge, UK: Burleigh Dodds Science Publishing. https://doi.org/10.1201/9781351114479
