Location: Soybean/maize Germplasm, Pathology, and Genetics Research
2022 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
This is the final report for this project which terminated April 2022. See the report for the replacement project 5012-22000-023-000D, "Identify and Characterize Resistance to Soybean Pathogens and Pests" for additional information.
For Objective 1, soybean growth was reduced when infested with soybean thrips and soybean vein necrosis virus. Soybean thrips are the primer vector of Soybean Vein Necrosis Virus (SVNV), a relatively recently discovered virus of soybean. Experiments were completed that showed the height, number of seeds and seeds weight were reduced 50%, 80% and 75%, respectively, when plants were infested with noninfected soybean thrips. For plants infested with SVNV-infected soybean plant height was reduced 78%, and plants died before reaching maturity reducing seeds and seed weights 100%.
For Objective 2, soybean germplasm lines with aphid resistance were developed. Soybean aphid is a serious pest in North America and infestations can cause economically significant losses to the soybean crop. Aphid resistance genes have been identified and deployed with some success; however, biotypes of the aphids are known that overcome single aphid resistance genes. In this research, in cooperation with University of Illinois scientists, gene pyramids with aphid resistance genes in different combination were evaluated for resistance to four soybean aphid biotypes. Those lines with the Rag6 (resistance to Aphis glycines) resistance gene and many gene pyramids showed a high level of resistance to all four aphid biotypes. The final product of this research is to release soybean germplasm with resistance gene pyramids that can be used to develop commercial cultivars that soybean growers could use to manage this pest.
New sources of soybean germplasm resistance to sudden death syndrome (SDS) of soybean. Host resistance is among the most sustainable tools to reduce losses to SDS, and screening soybean accessions for sources of resistance is a fundamental part of discovering host resistance. We have been in the process of summarizing results of evaluating 10,144 soybean plant introductions (PIs) for SDS resistance. Using a tiered testing sequence and a seedling layered inoculum method in the greenhouse, new sources of resistance were identified. In the last tier of testing, 16 PIs had mean foliar severity ratings not significantly different from PI 567374, the resistance check; five of the PIs had greater relative dry shoot, root, and total weight than PI 567374. The highly resistant entries reported here will be useful for further studies to understand the resistance mechanisms to Fusarium virguliforme and for breeding programs focused on increasing SDS resistance in elite breeding lines.
Evaluation of soybean germplasm for resistance to red crown rot. Red crown rot (RCR) of soybean is caused by Calonectria ilicicola, a soilborne fungus. The disease was reported in Illinois in 2019, and there is little information about sources of resistance to this disease or about resistant cultivars. The goal of this research is to discover sources of resistance in soybean to this fungus, determine the inheritance of the resistance, and develop germplasm with RCR resistance. Before sets of different types of soybean gemplasm can be evaluated for resistance, methods on how to inoculate and evaluate plants for resistance are needed. In our preliminary work, in cooperation with scientists at the University of Illinois, several subsets of soybean germplasm (elite soybean breeding lines and a subset of ancestral soybean lines) were evaluated using a layered inoculum technique. Root rot, post-emergence damping off, and foliar symptoms have been evaluated. There were differences in levels of resistance in some of the lines and more testing with different methods is still needed to verify this resistance.
Evaluation of soybean foliar diseases in African variety trials. In cooperation with University of Illinois and scientists located in Africa, multi-location soybean production trials have made it possible to identify soybean entries that are resistant to diseases across Africa. Through these trials (Pan African Soybean Variety Trials), soybean entries adapted to Africa were evaluated for incidence and severity of foliar diseases. The trials were established in multiple locations in six countries. A visual pre-transformed severity scale was used to evaluate the plants during the reproductive growth stages. Two bacterial diseases, seven fungal, one oomycete and one viral disease were observed in the soybean fields. The severity for the bacterial diseases was generally low. Cercospora leaf blight was the most common disease occurring in 30% of the entries. There were differences in severity ratings among some entries at some locations for Cercospora leaf blight, frogeye leaf spot, red leaf blotch and soybean rust. This data from these trials is being summarized with a target of submitting a manuscript on the results in the next fiscal year.
Accomplishments
1. Developed method to express foreign genes in plant parasitic nematodes to provide ability to disrupt specific biologically active targets within the pathogen, or the plant-pathogen interaction. Plant parasitic nematodes cause significant losses in crop production each year, yet little is known about the molecular basis for the interactions between plant and nematodes that lead to disease. It has been difficult to manipulate the expression of genes involved in these interactions because many plant parasitic nematodes reproduce sexually making it necessary to be able to track gene over multiple generations to ensure stably homozygous. Additionally, many of these plant pathogens require a specific host plant to grow and reproduce making it a challenge to manipulate in a laboratory. ARS researchers in Urbana, Illinois, cooperated with researchers at the University of Illinois and the University of Tennessee, and Chungnam National University in South Korea to describe the development of methods to express foreign genes in plant parasitic nematodes that utilizes brief high voltage electrical pulses allowing the uptake of genes by the parasitic nematodes. This method was successfully used with soybean cyst nematode, root-knot nematode and the free-living model nematode, Caenorhabditis elegans. The ability to transiently express genes in economically important plant parasitic nematodes provides a rapid means to evaluate nematode and/or foreign genes for their potential roles as nematicides or to interfere with nematode life cycles.
2. Determined precipitation change accentuates or reverses temperature effects on aphid dispersal resulting in possible increased spread of aphids. Rising temperatures and precipitation in some of the world’s most productive agroecosystems have the potential to greatly alter insect herbivore-plant interactions in ecologically and economically significant ways. To study this, ARS researchers in Urbana, Illinois, cooperated with researchers at the University of Illinois and the University of Georgia to observe more than a half of a million aphid observations from the U.S. Midwest Suction Trap Network. These were examined to determine how the phenology of three agriculturally important aphid species varied with seasonal temperature and precipitation between 2005 and 2019. Climate change projections with climate-aphid phenology models predicted shifts in aphid phenology by 2050 and 2080. While there is growing evidence that early flights of aphids are advancing in response to warming winters, little is known about how the many dimensions of aphid phenology will respond to the combined effects of changing temperature and precipitation. Overall, the climate-aphid models predict that changes in climate will extend the period of crop colonization for three aphid species, possibly leading to increased damage to soybean crops.
3. Surveyed nematodes in organically farmed soybean fields to identify potential impact on yield reduction. Plant-parasitic nematodes feed on soybean roots resulting in yield losses. Surveys of nematodes in certified organic soybean fields have been infrequent compared to surveys in non-organic soybean fields. ARS researchers in Urbana, Illinois, cooperated with researchers at the University of Illinois to conduct a nematode survey in certified organic soybean fields in northern and central Illinois to determine the frequency and population densities of plant-parasitic and free-living nematodes. Fields surveyed included both long-term, five years or longer rotation with soybean, and short-term, every three years with soybean. Common plant-parasitic nematode taxa included spiral, lesion, cyst, stunt, dagger, and pin nematodes. Among the taxa, spiral, lesion, and dagger nematodes were above previously reported damage threshold levels in some fields. Cyst nematode population densities were significantly higher in fields under short-term rather than long-term rotation with soybean. This knowledge will allow organic growers to make intelligent control decisions to mitigate yield loss to nematode damage.
4. Reported new records of aphids in industrial hemp production. Industrial hemp production in the USA is increasing, and with it the list of insects colonizing the crop that could lead to reduced plant vigor and plant production. In this research, ARS researchers in Urbana, Illinois, cooperated with researchers at the University of Michigan to report new records of three aphid species recovered on industrial hemp in East Lansing, Michigan in 2020. The aphid species identification was obtained through morphological characteristics and DNA barcoding. For the suction trap collections, between 2017 and 2020, the number of individual cannabis production sites detecting aphids increased, and as well as the number of sites with multiple weeks of detection. The timing of detection also changed over the years. In 2017, the first year of the surveys, aphids were only detected late in the season, but by 2019 and 2020, aphids were detected throughout the season. These changes likely reflect the increase in industrial hemp production in the landscape in the Midwestern US and informs growers that insect pest like aphids might increase as production spreads, and more frequent control sprays might be warranted.
5. Identified best management practice recommendations due to bruchids threatening soybean production in Sub-Saharan Africa. Soybean production in Sub-Saharan Africa has increased in recent years. Several abiotic and biotic stresses decrease yield, including pathogens and pests that attack seed. ARS researchers in Urbana, Illinois, cooperated with researchers at the Soybean Innovation Lab at the University of Illinois who focuses on improving soybean production across Africa, to report bruchid (also known as seed weevils) infested/damaged seed in seed lots in Cameroon, Malawi, Mozambique, and Rwanda. Adult bruchids discovered at the Malawi SIL location were identified as Callosobruchus chinensis. Bruchids are a destructive storage pest of legumes and monitoring the different species attacking soybean will help researchers and producers understand the potential threat of bruchids to soybean production in SSA as well as help implement the best management practices.
6. Characterized and compared intestinal bacterial microbiomes of stink bugs collected in Brazil and the United States. Herbivorous insects are one of the main biological threats to crops. One such group of insects, stink bugs, do not eat large amounts of tissue when feeding on soybean, but are very damaging to the quality of the seed yield as they feed on green developing seeds leading to poorly marketable harvests. In addition to causing physical damage during sucking-feeding activities, the insects can also transmit microbial pathogens, leading to even greater yield loss. ARS researchers in Urbana, Illinois, cooperated with researchers in Brazil to characterize the bacteria found within the red-banded stink bug collected in Brazil and the United States, as well as within the neotropical brown stink bug collected in Brazil. After quality filtering of the data, 192 samples were kept for analyses: 117 samples from the red-banded stink bug, covering three sites in Brazil and four sites in the United States, and 75 samples for the neotropical brown stink bug ,covering 10 sites in Brazil. The most interesting observations were that the diversity and abundance of some bacterial families were different in the different ecoregions of Brazil and the United States. Some families, such as Acetobacteraceae, Bacillaceae, Moraxellaceae, Enterobacteriaceae, and Rhodocyclaceae, may be related to the better adaptation in some localities in providing nutrients, break down cellulose, detoxify phytochemicals, and degrade organic compounds, which makes it difficult to control these species. Knowing the makeup of the insect intestinal microbiome can inform producers if there is need to worry about the possible spread of specific diseases, as well as help researchers identify microbes that might be essential for stink bug health.
7. Identified differences in the aggressiveness of five Pythium species and among isolates of some species. Several species of the oomycete genus Pythium cause seed rot and seedling damping-off (i.e., fatal wilting) of soybean. A trend toward earlier planting dates in recent decades has led to an increase in disease caused by Pythium pathogens. Using Petri plate and greenhouse experiments, ARS researchers in Urbana, Illinois, cooperated with researchers at the University of Illinois to rank the damage caused by the different Pythium species. Significant differences in aggressiveness were also found among isolates of the same species. Overall, the soybean cultivars ‘Archer’ and ‘Maple Glen’ had less disease than ‘Conrad’, ‘Maple Isle’ and ‘Sloan’, indicating the potential to develop more resistant cultivars by making crosses with more resistant parents. The identification of significant differences in aggressiveness illustrated the importance of screening germplasm and breeding material with Pythium isolates that are known to be aggressive representatives of their respective species. This knowledge can assist pathologists and breeders in their efforts to screen for Pythium resistant germplasm.
Review Publications
Crossley, M.S., Lagos-Kutz, D.M., Davis, T.S., Eigenbrode, S.D., Hartman, G.L., Voegtlin, D.J., Snyder, W.E. 2022. Precipitation change accentuates or reverses temperature effects on aphid dispersal. Ecological Applications. Volume 32, Issue 5, Article e2593. https://doi.org/10.1002/eap.2593.
Murithi, H.M., Pawlowski, M.L., Degu, T., Hunde, D., Malede, M., Obua, T., Mushoriwa, H., Coyne, D., Tukamuhabwa, P., Hartman, G.L. 2022. Evaluation of soybean entries in the Pan-African trials for response to Coniothyrium glycines, the cause of red leaf blotch. Plant Disease. 106:535-540. https://doi.org/10.1094/PDIS-05-21-1017-RE.
Lagos-Kutz, D.M., DiFonzo, C., Hartman, G.L. 2021. New records of aphids (Hemiptera: Aphididae) on industrial hemp in the US Midwest. Great Lakes Entomologist. 54:2, Article 9. https://scholar.valpo.edu/tgle/vol54/iss2/9.
Han, J., Ugarte, C.M., Nunez Flores, M., Hansen, M.G., Bowen, C.R., Schroeder, N.E., Hartman, G.L. 2021. Plant-parasitic and free-living nematodes from organically farmed fields in Illinois and Wisconsin. Plant Health Progress. 23:227-234. https://doi.org/10.1094/PHP-06-21-0096-S.
Han, J., Locke, S.P., Herman, T.K., Schroeder, N.E., Hartman, G.L. 2022. Evaluation of perennial Glycine species for response to Meloidogyne incognita, Rotylenchulus reniformis, and Pratylenchus penetrans. Journal of Nematology. 54:1-13.
Thekke Veetil, T., McCoppin, N.K., Domier, L.L., Hajimorad, M.R., Lambert, K.N., Lim, H., Hartman, G.L. 2022. Transient expression of a luciferase mRNA in plant-parasitic and free-living nematodes by electroporation. Molecular and Biochemical Parasitology. 250. Article 111489. https://doi.org/10.1016/j.molbiopara.2022.111489.
Pawlowski, M.L., Lagos-Kutz, D.M., Da Fonseca Santos, M., Lee, N., Chigeza, G., Nachilima, C., Francischini, J., Hartman, G.L. 2021. Potential threat of bruchids on soybean production in Sub-Saharan Africa. Plant Health Progress. 22:86-91. https://doi.org/10.1094/PHP-10-20-0093-MR.
Moro, M.S., Wu, X., Wei, W., Mendes, L.W., Allen, K.C., Pinheiro, J.B., Clough, S.J., Zucchi, M.I. 2021. Characterization and comparison of intestinal bacterial microbiomes of Euschistus heros and Piezodorus guildinii collected in Brazil and the United States. Frontiers in Microbiology. 12:769965. https://doi.org/10.3389/fmicb.2021.769965.
