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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #441689
Research Project: Practices for Management of Predominant Nematodes and Fungal Diseases for Sustainable Soybean Production

Location: Crop Genetics Research

2023 Annual Report


Objectives
1. Identify novel sources of resistance to existing and newly emerging soybean cyst nematode (Heterodera glycines, SCN) populations, and develop and deploy new soybean germplasm with broad resistance using traditional and marker-assisted breeding. 1.A. Phenotype Glycine max accessions available in USDA soybean germplasm collection for reaction to SCN populations and evaluate entries in Uniform Soybean Tests, Southern States for resistance to SCN. 1.B. Identify new sources of SCN resistance, pyramid resistance gene(s) for SCN, charcoal rot (CR), and frogeye leaf spot (FLS), and develop germplasm using molecular markers associated with resistance. 2. Determine host-pathogen interactions of fungal diseases in soybeans, including CR and FLS, identify new sources of resistance using improved screening methods, and develop innovative strategies for managing these diseases. 2.A. Identify new resistant soybean genotypes using improved screening methods against virulent pathotypes. 2.B. Evaluate the effects of cultural practices on CR and FLS severity and yield and develop alternate management practices for control of these diseases in soybean. 2.C. Evaluate the mechanism of defense in host pathogen interaction for CR. 3. Develop innovative methods and/or enhance existing methods to assay soil and root infection for improved plant-parasitic nematode detection, identification, and management, and design effective cultural methods for mitigating plant-parasitic nematodes in grower fields. 3.A. Evaluate existing and novel methods to increase detection and screening of plant-parasitic nematodes. 3.B. Determine the impacts of cultural practices and resistance on plant-parasitic and free-living nematodes to ascertain information about soil health and yield.


Approach
Identify and characterize new sources of resistance to nematode and fungal diseases of soybean that will potentially broaden diversity among resistance genes in soybean cultivars and may provide more durable resistance. New soybean germplasm lines with combined resistance will be developed in maturity groups IV and V with resistance to soybean cyst nematode, root-knot nematode, frogeye leaf spot, charcoal rot, as well as other fungal pathogens. Parasitic and free-living nematode communities will be characterized in soybean fields, especially those with corn and/or cotton in the rotation. New or enhanced methods to detect plant-parasitic nematodes in soil or roots will be developed. Valuable data for the reaction of breeding lines to nematode populations will be available to be utilized by the breeders for potential release to public and private sectors. The new releases in combination with effective cultural practices will also be developed and made available to the public to manage nematode and fungal population shifts.


Progress Report
Progress was made on all three objectives, and work will continue to identify new sources of resistance as well as cultural management options for soybean cyst nematode (SCN) populations, charcoal rot and frogeye leaf spot and to incorporate the resistance into new varieties of soybean for growers in Tennessee and other southern states. ARS researchers at Jackson, Tennessee, are making progress related to developing soybean with resistance to one or more diseases. One hundred germplasm lines were screened for reaction to HG Type 1.2.5.7 and one line was rated as moderately susceptible and 99 lines as susceptible. None of the lines were resistant or moderately resistant. Results of this work will be summarized along with those of the HG Type 2.5.7 screening that was accomplished in 2021. This progress is related to Subobjective 1A. Two hundred seventy-three recombinant inbred lines were screened for reaction to SCN HG Type 2.5.7. Additionally, 64 lines were screened for reaction to HG Type 1.2.5.7 for the Tennessee Soybean Variety tests. The latter work resulted in an extension publication. This progress is related to Subobjective 1A. Screening of Uniform Soybean Tests for Southern States for reaction to SCN populations was conducted in 2022. Screening was done with 2,500 SCN eggs of HG Types 2.5.7 and 1.2.5.7 on 298 soybean lines and after 30 days the ratings based on number of cysts on the roots. Mostly susceptible reaction ratings were recorded. This work was summarized in the Uniform Soybean Tests – Southern States 2022 report. This progress is related to Subobjective 1A. Breeding for new soybeans with robust disease resistance continues to be a major focus. In 2022, a comprehensive breeding pipeline focused on soybean disease resistance was evaluated in the field by ARS researchers in Jackson, Tennessee. This included newly imagined cross combinations, breeding nurseries for population advancement, and yield testing of advanced lines. Five elite soybean lines from outside USDA were accessed through material transfer agreements for use in crossing. Further, diverse, and novel sources of diseases resistance were accessed through the Germplasm Resources Information Network, including NRS100 (PI 578345), a wild soybean relative (Glycine soja) with novel SCN resistance. All these new lines were paired for cross combinations with each other and existing soybean lines within the program with the goal of improving yield while advancing disease resistance in Mid-South adapted soybeans. Seed from these novel cross combinations will serve as the foundation for future improvements in the soybean breeding program. These advancements are directly related to Subobjective 1.B. Further, in 2022, over 200 plant rows ranging from F1 to F6 and beyond were growing in breeding nurseries for population advancement. These populations were sourced from novel sources of SCN resistance that would reduce the pressure on the currently overused source or resistance widely used in the U.S., PI 88788. The novel sources of SCN resistance found in these breeding populations include PI 567516C, PI 437655, and PI 494182, as well as ‘Hartwig’, which has served as a highly effective source of SCN resistance in the Mid-South. In addition to robust SCN resistance, many of these populations possess other highly impactful traits, including resistance to frogeye leafspot, charcoal rot, and moderate yield potential. In 2022, over 50 high potential soybean breeding lines were tested in replicated, multi-environment field trials in Jackson and Milan, Tennessee in maturity groups IV-early, IV-late, and V. High performers from these tests advance into regionwide field testing, such as the USDA Southern Uniform Test, where they gain exposure to a wide audience of plant breeders, and can be accessed through agreement for future crossing and development of high potential soybean lines. These efforts supported Subobjective 1.B. In addition to the field breeding efforts, 2022 was an important year for molecular breeding. Over 1,000 soybean leaves were collected for DNA extraction and molecular analysis from the population rows and the yield trials. Using a newly acquired Roche Lightcycler 96 SNP genotyping machine, these samples will be evaluated for genetic resistance to SCN and fungal diseases. Through molecular breeding, pyramiding multiple sources of resistance for SCN can be accomplished. This technique is not possible using phenotyping alone and allows for highly robust SCN resistance which is much more challenging for resistance breaking. Further, molecular breeding allows for efficient, early-stage screening of breeding population assists with population advancement decisions,confirmation of resistance in late-stage breeding lines that are further along in testing, and ease of combining multiple disease resistances, such as SCN and frogeye leaf spot through pyramiding strategies. Using the most advanced, SNP based genotyping technology further improves this process. This progress is in relation to Subobjective 1.B. The second year of a field trial was conducted in two locations (Jackson and Milan, Tennessee) with low and high SCN pressure, respectively. Treatments were soybean seed sources derived from: susceptible; PI 88788; PI 548402; 50% susceptible and 50% PI 88788; 50% susceptible and 50% PI 548402; 50% PI 88788 and 50% PI 548402; and 33% susceptible, 33% PI 88788, and 33% PI 548402. Plots with the three-way mix had greater SCN fecundity (147 eggs/cyst) than the PI 88788/PI 548402 treatment (24 eggs/cyst) in the high SCN pressure site in 2022, yet there were no significant differences in yield. Data from the past two years of these trials will be published in a manuscript. Additionally, soil samples from this work were subjected to two different nematode extraction methods – elutriation and sucrose-centrifugation – to determine efficiency of these methods for recovering SCN from field samples. This progress is related to Subobjectives 1C and 3A. Soybean lines were evaluated for charcoal rot and frogeye leaf spot resistance in 2022. Among the 109 Roundup Ready lines evaluated, 11 lines were identified to have full resistance and 12 lines had moderate resistance, while 24 conventional breeding lines were identified as moderately resistant. In addition, single-row selections from 400 inbred lines that were derived from various crosses were selected for charcoal rot resistance and 13 lines identified as having a high level of resistance with good agronomic traits and will be advanced for future breeding programs. Similarly, 72 soybean lines were screened for frogeye leaf spot resistance in Milan, Tennessee, in a field that was irrigated beginning at flowering using a central pivot. The location has a known natural infection every year and the rating based on percentage of leaf area covered by frogeye leaf spot. Results showed that 10 lines had no sign of infection and 47 lines had less than 2% infection and are considered moderately resistant. This screening identified alternative sources of resistance to those lines derived from the cultivar ‘Davis’, the source of resistance for all current commercial cultivars. Their genetic information was characterized using a marker-trait association analysis and these selections will be advanced for future breeding and public release. This progress is related to Subobjective 2A. Work to combine resistance to multiple diseases into a single soybean line continued in 2022. Unique advanced progenies derived from previously made crosses to combine resistance to soybean cyst nematode, charcoal rot, and frogeye leaf spot were evaluated in the field. We are also evaluating the impact of row spacing and seeding rate on charcoal rot severity and yield. A manuscript on charcoal rot severity and soybean yield responses to planting date, irrigation and genotypes has been completed and published. Also, a manuscript on the effects of cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield under no-till system was submitted. This progress is related to Subobjectives 1B and 2B. Plant-associated microbes in and around the rhizosphere may function as an additional layer of defense against pathogens through suppressing the proliferation of pathogens by producing antimicrobial compounds or through niche competition. Four moderately resistant and four susceptible genotypes are used to measure the population of the charcoal rot fungus in the rhizosphere soil and in plant tissue. From the same soil samples microbial population and nematodes have been assessed over the last two years. In 2023, which will be the third year of the study, the research will be completed and assessed. The analysis may provide results to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. This progress is related to Subobjective 2C. A field trial was established in Jackson, Tennessee, consisting of three factors: cover crop mixes, burndown timing of the cover crop, and soybean seed treatment. Four soil sampling dates were assessed and nematodes (plant-parasitic and free-living), soil faunal community (rotifers, tardigrades, mites, oligochaetes, collembola), and charcoal rot colony-forming units were enumerated. The objective was to determine the potential benefits/disadvantages of using cover crops in relation to plant-parasitic nematodes and soil faunal communities in soybean production systems. Late burndown increased the reproduction of fungivores and bacterivores and SCN. The combination seed treatments performed better than the standalone insecticide and fungicide treatments in terms of soybean yield. This trial is being repeated in 2023. This progress is related to Subobjectives 2B and 3B.


Accomplishments
1. Charcoal severity is affected by planting date, irrigation and resistance of genotypes. Soybean production is influenced by planting date but its impact on yield in fields infested with charcoal rot fungus under varying environments is unknown. ARS researchers in Jackson, Tennessee, conducted research to detected that disease severity for the May planting date was significantly lower compared to April and June planting. Correspondingly, yield for the April planting date was significantly lower than that of May and June in both irrigated and non-irrigated environments. Soybean lines interacted with planting date differently, however, selected moderately resistant lines showed the greatest yields in early May to early June planting with increased yield in charcoal rot infested environments. Interestingly, the yield of susceptible lines increased significantly with each subsequent planting date. These results could fill the knowledge gaps in the current soybean production system that need to be incorporated into the future farming practice that growers need to consider when planting soybean in fields infested with the charcoal rot fungus.

2. Role of seed sugars as a mechanism of charcoal rot disease resistance identified. Charcoal rot is a major disease of soybean that causes significant yield loss and poor seed quality. Currently, there are no resistant soybean cultivars in the market, and the genetic defense mechanism controlling this disease is unknown. In collaboration with other ARS researchers, ARS researchers in Jackson, Tennessee, investigated the role of soybean seed sugars in moderately resistant and susceptible soybean genotypes. Our results showed that both moderately resistant and susceptible genotypes had a wide range of sugar levels. The moderately resistant genotypes however, had the ability to maintain higher levels of sucrose, glucose, and fructose that are desirable for taste and flavor; while the susceptible genotypes showed higher levels of stachyose with lower levels of sucrose, glucose, and fructose that are undesirable and considered anti-nutritional components. The response of susceptible genotypes with higher levels of undesirable sugars may reflect the possible role of these sugars in the defense mechanism to charcoal rot in soybean. The ability to maintain higher levels of sucrose, glucose, fructose in moderately resistant genotypes reflects healthier xylem and phloem tissue conducting system and active sugar enzymes. This research provides new knowledge on seed sugars and their role as biological markers in the soybean defense mechanism of the moderately resistant and susceptible genotypes to charcoal rot. It further helps scientists understand the impact of charcoal rot and irrigation environment on seed sugars, using moderately resistant and susceptible genotypes.

3. Improved MG IV soybean germplasm line (DS1260-2) with tolerance to mature seed damage. Mature seed damage occurs when plants are subjected to hot humid conditions during plant maturation and dry down. Mature seed damage results in price discounts when grain is sold and can cause economic loss to producers in the southern U.S., as well as in other hot humid production environments. ARS researchers in Stoneville, Mississippi, Jackson, Tennessee, and West Lafayette, Indiana, developed an improved MG IV soybean germplasm line that has significantly less seed damage with significantly higher seed germination, less Phomopsis seed decay, and less toxins from fungi than commercial cultivars. This is the first improved U.S. soybean germplasm release that addresses mature seed damage. Seed of DS1260-2 had significantly lower Phomopsis seed decay and toxins in comparison to commercial cultivars. This germplasm will be provided to soybean breeders and other scientists worldwide and can be a resource for cultivar development.

4. A soybean cyst nematode diagnostic guide was developed and released. The soybean cyst nematode is one of the most economically important pathogens of soybean. The species impacts soybean production worldwide and causes significant yield loss even in the absence of visible aboveground symptoms. While there are numerous articles about this pathogen, a condensed, peer-reviewed diagnostic guide was needed to better summarize this information. An ARS researcher in Jackson, Tennessee, helped develop a diagnostic guide that described the host range, signs, symptoms, and geographic distribution of soybean cyst nematode, as well as included information regarding pathogen identification, storage, and pathogenicity tests for this nematode. Information on cultural practices to effectively manage soybean cyst nematode was developed and released to the scientific community. Additionally, scientists benefitted from this work as a basis for further investigations, such as understanding the implications of resistance and cultural management on soybean cyst nematode population health and fitness.

5. Maturity groups IV and higher are more susceptible to soybean cyst nematode than earlier maturity groups (000-III). The continued search for new sources of soybean cyst nematode resistance remains crucial in fighting this pathogen. Soybean varieties are marketed with combinations of traits and the need for annual testing for reaction to multiple populations of soybean cyst nematode is warranted (i.e., HG Types 2.5.7 and 1.2.5.7). Greenhouse trials with collaborators were conducted by ARS researchers in Jackson, Tennessee, in 2022 (USDA soybean germplasm screening, Uniform Soybean Tests, Southern States, and Tennessee soybean variety tests). One hundred Glycine max germplasm lines from the USDA soybean germplasm collection were obtained and screened for reaction to soybean cyst nematode HG Type 1.2.5.7, determining the following: 0 lines with resistance; 0 lines with moderate resistance; 1 line with moderate susceptibility; and 99 lines with susceptibility. For the Uniform Soybean Tests, Southern States, 298 entries were tested for reaction to HG Types 2.5.7 and 1.2.5.7 in 2022, resulting in mostly susceptible reactions to soybean cyst nematode for maturity groups IV through VIII. Out of 56 soybean varieties available to growers in Tennessee in 2022, mostly susceptible reactions to soybean cyst nematode HG Type 1.2.5.7 for maturity groups IV and V were observed.


Review Publications
Oliveira, C.J., Van Santen, E., Marin, M., Schumacher, L.A., Peres, N.A., Desaeger, J. 2023. Susceptibility of seven strawberry cultivars to Belonolaimus longicaudatus and interaction with Phytophthora cactorum. Nematology. 2023:1-12. https://doi.org/10.1163/15685411-bja10237.
 Mengistu, A., Kelly, H.M., Read, Q.D., Ray, J.D., Bellaloui, N., Schumacher, L.A. 2023. Charcoal rot severity and soybean yield responses to planting date, irrigation, and genotypes. Plant Disease. https://doi.org/10.1094/PDIS-06-22-1329-RE.
 Schumacher, L.A., Grabau, Z.J., Wright, D.L., Small, I.M., Liao, H. 2022. Effects of grass-based crop rotation, nematicide, and irrigation on the nematode community in cotton. Journal of Nematology. 54(1):3922. https://doi.org/10.2478/jofnem-2022-0046.
 Fritz, L.A., Arelli, P.R., Young, L.D., Mengistu, A., Gillen, A.M. 2022. Registration of conventional soybean germplasm JTN-5110 with resistance to nematodes and fungal pathogens. Journal of Plant Registrations. 17:189-201. https://doi.org/10.1002/plr2.20254.
 Chen, P., Shannon, J.G., Vieira, C.C., Nascimento, E.F., Ali, M.L., Lee, D., Scaboo, A., Crisel, M., Smothers, S., Clubb, M., Selves, S., Nguyen, H., Li, Z., Mitchum, M.G., Bond, J.P., Meinhard, C.G., Usovsky, M., Li, S., Gillen, A.M., Smith, J.R., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T., Moseley, D. 2022. Registration of ‘S16-3747GT’: A high-yielding determinate maturity group V soybean cultivar with broad biotic and abiotic stressors tolerance. Journal of Plant Registrations. 16:550-563. https://doi.org/10.1002/plr2.20222.
 Chen, P., Shannon, G., Lee, D., Granja, M.D., Vieira, C., Lee, Y., Ali, L., Nascimento, E.D., Scaboo, A.L., Crisel, M.W., Smothers, S.W., Clubb, M.M., Selves, S.W., Nguyen, H.P., Li, Z., Mitchum, M.G., Averitt, B., Bond, J., Meinhard, C.T., Usovsky, M., Li, S., Smith, J.R., Gillen, A.M., Mengistu, A., Zhang, B., Mozzoni, L., Robbins, R.T., Moseley, D. 2023. Registration of ‘S17-2243C’: A non-genetically modified maturity group IV soybean cultivar with high yield and elevated oil concentration. Journal of Plant Registrations. 17:318-328. https://doi.org/10.1002/plr2.20276.
 Chen, P., Shannon, J.G., Lee, D., Granja, M.O., Ali, M.L., Vieira, C.C., Lee, Y., Nascimento, E.D., Scaboo, A., Crisel, M., Smothers, S., Clubb, M., Selves, S., Nguyen, H.T., Li, Z., Mitchum, M.G., Averitt, B., Bond, J.P., Meinhardt, C.G., Usovsky, M., Li, S., Smith, J.R., Gillen, A.M., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T., Moseley, D. 2023. Registration of S16-11644C soybean cultivar with high-yielding performance and broad disease resistance. Journal of Plant Registrations. 17:67-79. https://doi.org/10.1002/plr2.20274.
 Lazicki, P.A., Lee, J., Mengistu, A., Jagadamma, S. 2023. Drought, heat, and management interact to affect soil carbon and nitrogen losses in a temperate, humid climate. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2023.104947.
 Bellaloui, N., Mengistu, A., Smith, J.R., Abbas, H.K., Accinelli, C., Shier, W.T. 2023. Soybean seed sugars: A role in the mechanism of resistance to charcoal rot and potential use as biomarkers in selection. Plants. 12:1-14. https://doi.org/10.3390/plants12020392.
 Mahecha-Garnica, S., Ye, W., Schumacher, L.A., Gorny, A.M. 2022. Soybean cyst nematode of soybean: A diagnostic guide. Plant Health Progress. 23:507-513. https://doi.org/10.1094/PHP-11-21-0138-DG.