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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #432488
Research Project: Genetics and Management of Newly Emerging Soybean Cyst Nematodes and Predominant Fungal Diseases for Sustainable Soybean Production

Location: Crop Genetics Research

2022 Annual Report


Objectives
Objective 1: Identify sources of resistance to newly emerging soybean cyst nematode populations, develop new soybean germplasm with resistance, and develop methods for managing soybean cyst nematodes in soybeans using traditional and marker assisted breeding methods. Subobjective 1a. Phenotype Glycine max accessions available in USDA soybean germplasm collection for reaction to SCN populations. Identify new/additional sources of resistance, characterize for unique resistance genes and develop molecular markers associated with resistance. Subobjective 1b. Pyramid nematode resistance genes into elite backgrounds of maturity groups IV and V in combination with resistance to charcoal rot and Frogeye leaf spot to develop new germplasm/cultivars. Subobjective 1c. Determine the effect of soybean cyst nematode in combination with other plant-parasitic nematodes on crop damage in Mid South soybean production fields. Subobjective 1d. Evaluate entries in USDA Uniform Soybean Tests for Southern States and ARS breeding lines for reaction to SCN. Objective 2: Determine mechanisms underlying host-pathogen interactions in soybean for the fungal diseases charcoal rot and frogeye leaf spot, identify new sources of resistance in soybean to these diseases using improved screening methods, and develop methods for managing these fungal diseases using traditional and marker assisted breeding methods. Subobjective 2a. Evaluate and identify new sources of germplasms, breeding lines, and cultivars for charcoal rot and frogeye leaf spot resistance in stress and non-stress environments for use in breeding programs. Subobjective 2b. Evaluate the effects of cultural practices on charcoal rot and frogeye leaf spot severity and yield and develop alternate management practices for control of these diseases in soybean.


Approach
Identify new sources of resistance to nematode populations in soybean that will potentially broaden diversity among resistance genes in soybean cultivars and may provide more durable resistance. New soybean germplasm line or lines will be developed in two different maturity groups IV and V with resistance to soybean cyst nematode, frogeye leaf spot, and charcoal rot, as well as other fungal pathogens, nematodes and insect pests. Nematodes will be found in soybean fields, especially those with corn and/or cotton in the rotation. 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. New accessions and germplasm lines with resistance to charcoal rot and frogeye leaf spot will be identified and released.


Progress Report
This is the final report for project 6066-21220-013-000D. In February 2022, it was replaced by project 6066-21220-015-000D titled “Practices for Management of Predominant Nematodes and Fungal Diseases for Sustainable Soybean Production.” Progress was made on both objectives for this long-term research project. We continued working to identify new sources of resistance to 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. Toward this end, ninety-nine germplasm lines (50 seeds per line) were obtained from the USDA soybean germplasm collection and screened for reaction to HG Type 2.5.7 and 5 lines were rated as moderately resistant; 27 lines were rated as moderately susceptible and 27 lines as susceptible. None of the line were resistant. Work will continue with these same lines for their reaction to HG Types 0 and 1.2.5.7 in 2022. This progress is related to Sub-objective 1A. A major concern in the breeding effort for SCN resistance is the trend of reduced effectiveness in the primary source of resistance in commercial soybean cultivars, PI 88788. For this reason, we focus our SCN resistance breeding efforts on soybeans derived from several sources, each providing greater protection against SCN than PI 88788. From 2017-2021, hundreds of plant rows from different breeding populations were grown at the research station in Jackson to advance the breeding pipeline. New sources were identified as SCN resistant and resistant to charcoal rot and frogeye leafspot with high yield potential. Germplasm lines such as JTN-5203 has been developed and released for its broad resistance for its soybean cyst nematode, reniform nematode and major fungal diseases combined with high yield potential and has been used as a standard resistant check in USDA Soybean Uniform Tests Southern States. Due to the high cost of commercially available herbicide tolerant soybean seed for planting, some of the growers in Arkansas, Missouri, North Carolina, and Kentucky, have used JTN-5203 to plant in their fields. In addition, four other lines were developed and released: JTN-5316, JTN-5416, JTN-5516 and JTN-5110. These four lines are in maturity group V and provide breeders with parent material containing durable resistance. Two additional MG IV lines that are developed and derived from PI 494182 and PI 437655 also merit consideration as germplasm releases. These releases will allow breeders to gain access to our improved germplasm and continue the breeding process to develop elite cultivars with outstanding disease resistance, which ultimately benefits both producers and consumers of soybeans and soy products. This time-consuming process of pyramiding resistance to SCN and fungal diseases into high yielding soybean germplasm is highly important and will continue with our program moving forward. The progress described above is related to Sub-objective 1B. A field trial was established in two locations (Jackson, Tennessee and Milan, Tennessee) with low and moderate SCN pressure, respectively, based on preliminary soil sampling. 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. Plant-parasitic nematodes recovered from soil samples included SCN, lesion nematode, lance nematode, and spiral nematode. Preliminary results from the Jackson, Tennessee, location in 2021 showed that the 50% susceptible and 50% PI 548402 treatment gave the highest soybean yield while the 33% susceptible, 33% PI 88788, and 33% PI 548402 treatment gave the greatest reduction in SCN population densities. For the Milan, Tennessee location, the greatest yield and lowest SCN population densities were from the PI 548402 treatment. The trials are being repeated in 2022. This progress is related to Sub-objective 1C. Two hundred seventy-three recombinant inbred lines were obtained from plant breeders in Stoneville, Mississippi, for reaction to SCN populations. Fifty percent of the lines have been screened for reaction to HG Type 2.5.7 and work will continue to complete the remaining lines as well as screen all lines for reaction to HG Types 0 and 1.2.5.7. Additionally, 56 lines were screened for reaction to HG Type 1.2.5.7 for the Tennessee Soybean Variety tests. This work resulted in an extension publication. This progress is related to Sub-objective 1D. Screening of Uniform Soybean Tests for Southern States for reaction to SCN populations was conducted in the greenhouse at the USDA-ARS Crop Genetics Research Unit in Jackson, Tennessee in 2021. Screening was done with 2,500 SCN eggs of HG Types 0, 2.5.7, and 1.2.5.7 on 324 soybean lines and after 30 days the ratings based on number of cysts on the roots. This work was summarized in the Uniform Soybean Tests – Southern States 2021 report. This progress is related to Sub-objective 1D. Based on a new disease assessment technique for rating frogeye leaf spot, field isolates of frogeye leafspot from wide geographical locations were evaluated and were classified into five groups, Pathogenicity group 1 through Pathogenicity group 5. Such grouping has three important uses: (1) document changes among field isolates, (2) enable specific management recommendations, and (3) identify resistant cultivars/germplasms. In addition, out of the 120 SCN resistant accessions obtained from the USDA National Genetic Resources Program, 12 were identified to have combined resistance for soybean cyst nematode and charcoal rot. These accessions will be valuable source for gene pyramiding in our breeding program. This progress is related to Sub-objective 2A. A three-year study on the effect of planting date on charcoal rot severity and yield has been completed. Although the current production system encourages early April planting, we determined that early May to early June is actually a better planting window to lower charcoal rot severity and increase yield in infested fields. We evaluated resistance to charcoal rot in a set of 120 soybean accessions reported to have resistance to one or more races of soybean cyst nematode and identified 12 accessions with combined resistance to races of soybean cyst nematode and charcoal rot. This study has been completed and the result has been published. The results from these studies will be used to improve crop management recommendations to better manage these diseases. This progress is related to Sub-objectives 1A and 2B. Work to combine resistance to multiple diseases into a single soybean line continued in 2021. Unique advanced progenies derived from previously made crosses to combine resistance to SCN, charcoal rot, and frogeye leaf spot were evaluated in the field for charcoal rot and frogeye leaf spot resistance. We are also evaluating the impact of cultural practices such as tillage, row spacing and seeding rates impact on charcoal rot severity and yield. This progress is related to Sub-objectives 1B and 2A. A set of soybean lines was evaluated for charcoal rot and frogeye leaf spot resistance. This study is a long-term research project and stakeholders are updated on the findings yearly at their meetings and field days. Among the 109 lines of Roundup Ready cultivars that were evaluated in 2021, 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 have been identified as having a high level of resistance to charcoal rot with good agronomic traits. These selections will be advanced for future breeding programs. Similarly, 72 soybean lines were screened for frogeye leaf spot resistance at the Research and Education Center in Milan, Tennessee, in a field that was irrigated beginning at flowering using a central pivot system. The test location has a known natural infection every year and the ratings were 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. The later are considered moderately resistant. This screening was intended to identify alternative sources of resistance to those lines derived from the cultivar ‘Davis’, the source of resistance for all current commercial cultivars. Their genetic information has been characterized using a marker-trait association analysis. These selections will be advanced for future breeding and public germplasm release. This progress is related to Sub-objective 2A. 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 the soil faunal community as well as charcoal rot enumerated. Four types of plant-parasitic nematodes (SCN, lesion nematode, lance nematode, and spiral nematode) were recovered from soil samples. Non-target (i.e., fungivores, bacterivores, rotifers, tardigrades, and oligochaetes) were always greater in early burn down plots compared to late burn down plots based on the spring sampling date. Charcoal rot colony forming units were greatest in the spring sampling. Soybean cyst nematode eggs per cyst were greatest in the insecticide, fungicide, and nematicide treatment based on the summer sampling date. This trial is being repeated in 2022. This progress is related to Sub-objectives 1C and 2B.


Accomplishments
1. Seven breeding lines with high oil content, broad disease resistance, and high yield potential registered. Soybean growers are constantly faced with yield losses caused by several fungal and plant parasitic nematodes. ARS researchers in Jackson, Tennessee, collaborated with researchers at the University of Missouri to meet the growing demand from growers and industry for high-yielding soybean germplasm with broad disease resistance and elevated oil and meal protein contents. The breeding progenies for each cross were tested in multiple environments across the United States including at the USDA location in Jackson, Tennessee, to identify disease resistance. These are, 'S13-1955C', S13-3851C’, ‘ShowMeSoy 4301’, ‘S13-10592C’, ‘S15-10434C’, ‘S16-11651C’ and ‘S16-5540GT’. All these lines have high oil content, broad disease resistance package and wide adaptation that make them an excellent choice for Midsouthern soybean growers.

2. Improved maturity group IV soybean germplasm line with tolerance to mature seed damage released. Mature seed damage (visual mold, insect feeding, discoloration, weathering, etc.) occurs when ripe soybean seed remains unharvested and subjected to seed pathogens and insects under hot humid conditions. Damaged seed is discounted when sold by farmers, resulting in immediate financial losses, is unfit for sowing, resulting in future financial losses to seed producers, and is less desirable to grain processors, resulting in further financial losses, both domestically and internationally. 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 DS31-243 were provided to southern soybean breeders through MTAs for cultivar development and will be deposited in the USDA soybean germplasm collection for use by scientists worldwide.


Review Publications
Zhang, K., Schumacher, L.A., Maltais-Landry, G., Grabau, Z., George, S., Wright, D., Small, I., Liao, H. 2021. Integrating perennial bahiagrass into the conventional rotation of cotton and peanut enhances interactions between microbial and nematode communities. Applied Soil Ecology. 170(2022). Article 104254. https://doi.org/10.1016/j.apsoil.2021.104254.
 Mengistu, A., Bellaloui, N., Arelli, P.R. 2021. Resistance to charcoal rot identified within soybean cyst nematode resistant accessions. Plant Health Progress. 1-8. https://doi.org/10.1094/PHP-01-21-0004-RS.
 Fritz, L.A., Arelli, P.R., Mengistu, A. 2021. Registration of three soybean germplasms with novel cyst nematode resistance from PI 567516C. Journal of Plant Registrations. 15:588-599. https://doi.org/10.1002/plr2.20166 .
 Chen, P., Shannon, G., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Ali, L.M., Lee, D., Nguyen, H.T., Li, Z., Mitchum, M., Bond, J.P., Meinhardt, C.G., Klepadlo, M., Li, S., Mengistu, A., Robbins, R.T. 2022. Registration of ‘S13-3851C’ soybean as a high-yielding conventional cultivar with high oil content and broad disease resistance and adaptation. Journal of Plant Registrations. 16:21-28. https://doi.org/10.1002/plr2.20098.
 Bellaloui, N., Smith, J.R., Ray, J.D., Mengistu, A., Gillen, A.M., Fisher, D.K., Singh, G. 2022. Responses of seed yield, quality, and composition to the harvest-aid paraquat in soybean grown in Mississippi. Agrosystems, Geosciences & Environment. 5(2):e20262. https://doi.org/10.1002/agg2.20262.
 Chen, P., Shannon, G., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Ali, L.M., Lee, D., Nguyen, H.T., Li, Z., Mitchum, M.G., Bond, J.P., Meinhard, C.G., Usovsky, M., Li, S., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T. 2022. ‘ShowMeSoy 4301’: High yielding soybean with multiple disease resistance and elevated oil content. Journal of Plant Registrations. 16:276-286. https://doi.org/10.1002/plr2.20207.
 Chen, P., Shannon, G., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Ali, L.M., Lee, D., Nguyen, H.T., Li, Z., Mitchum, M.G., Bond, J.P., Meinhard, C.G., Usovsky, M., Li, S., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T. 2022. Registration of ‘S13-10592C’: a soybean cultivar with resistance to multiple diseases and high oil content. Journal of Plant Registrations. 16:252-261. https://doi.org/10.1002/plr2.20182.
 Chen, P., Ali, L.M., Shannon, G., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Lee, D., Scaboo, A.M., Nguyen, H.T., Mitchum, M.G., Li, Z., Bond, J.P., Meinhard, C.G., Li, S., Mengistu, A., Robbins, R.T., Mozzoni, L.A., Zhang, B., Smith, J.R., Buckley, B. 2022. Registration of ‘S16-5540GT’ soybean cultivar with high yield, resistance to multiple diseases, elevated protein content and wide adaptation. Journal of Plant Registrations. 16:262-275. https://doi.org/10.1002/plr2.20201.
 Chen, P., Ali, L.M., Shannon, G., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Lee, D., Scaboo, A.M., Nguyen, H.T., Mitchum, M.G., Li, Z., Bond, J.P., Meinhard, C.G., Li, S., Mengistu, A. 2022. Registration of ‘S15-10434C’ soybean cultivar with high yield, resistance to multiple diseases and wide adaptation. Journal of Plant Registrations. 16:234-245. https://doi.org/10.1002/plr2.20164.
 Chen, P., Ali, L.M., Shannon, G., Vieira, C., Lee, D., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Scaboo, A.M., Usovsky, M., Nguyen, H.T., Mitchum, M.G., Li, Z., Bond, J.P., Meinhard, C.G., Li, S., Gillen, A.M., Mengistu, A., Robbins, R.T., Mozzoni, L.A., Zhang, B., Smith, J.R., Buckley, B., Moseley, D. 2022. Registration of ‘S16-11651C’ as a conventional soybean cultivar with high yield, resistance to multiple diseases and broad adaptation. Journal of Plant Registrations. 16:329-340. https://doi.org/10.1002/plr2.20224.