Skip to main content
ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Research Project #435273
Research Project: Evaluation and Development of Improved Soybean Germplasm, Curation of USDA Accessions and Regional Evaluations of New Genotypes

Location: Crop Genetics Research

2023 Annual Report


Objectives
Objective 1. Develop and release novel, genetically diverse soybean germplasm with improved yield, seed quality, and tolerance to abiotic and biotic stresses that are well suited for sustainable production, especially in the southern United States. Objective 2. Identify and characterize traits and genes influencing soybean plant health and physiology, including seed quality and agronomic traits in southern U.S. environments, and develop breeder-friendly selection methodologies. Sub-Objective 2.A. Determine the inheritance and genomic location of new genes influencing or affecting resistance to Phomopsis seed decay (PSD) and investigate the effect of PSD on seed composition. Sub-Objective 2.B. Determine the inheritance and genomic location of new genes influencing or affecting heat-tolerant seed production and investigate the effect of heat stress on seed composition and quality. Objective 3. Conserve available soybean genetic resources and maintain genetic integrity within the southern USDA Soybean Germplasm Collection, as well as characterize and evaluate new accessions. Objective 4. Plan, manage and coordinate the Uniform Soybean Tests - Southern States, including seed distribution, data compilation and analysis, and timely publication of phenotypic information useful for selection and generation advancement.


Approach
The long-term objective of this project is to develop soybean [Glycine max (L.) Merr.] germplasm that will ameliorate the adverse effects of biotic and abiotic stresses in order to increase seed yield, yield stability, and seed quality in the mid-southern U.S. The research of the five scientists assigned to the project emphasizes identification and development of disease resistant germplasm and heat tolerant germplasm with a focus on seed quality and composition. The inheritance of disease and heat related traits will be determined and the underlying genes controlling tolerance/resistance molecularly mapped. These traits will be combined with other disease resistance, quality and physiological traits into high-yielding adapted germplasm. Where possible exotic germplasm will be incorporated into new germplasm to increase genetic diversity. Newly developed germplasm will be fully characterized and relationships of traits to multiple abiotic and biotic stresses elucidated. Physiological, pathological and molecular methodologies and techniques will be developed or refined to characterize complex soybean traits. Seed for maturity groups V-VIII in the USDA soybean germplasm collection will be maintained and new accessions evaluated and characterized. We will coordinate regional testing of new public soybean breeding lines, analyze data and publish results annually.


Progress Report
This project has ended and will be replaced by the new project 6066-21220-015-000D, “Breeding Stress Tolerant Soybeans, Regeneration and Evaluation of USDA Germplasm Collection, and Management of Uniform Soybean Trials.” Improved germplasm lines LG03-4561-14, DS5-67, and DS31-243 were released by this project in 2018, 2020, and 2022, respectively, with 25%, 50%, and 25% exotic parentage, respectively. LG03-4561-14 and DS31-243 are competitive for yield with commercial cultivars of corresponding maturities (late III and early IV, respectively) under early plantings in the Mid-South. Rust-resistant DS5-67 is competitive for yield with cultivars of corresponding maturity (mid V) under severe rust pressure. LG03-4561-14 was the first improved germplasm line derived from PI 445837 and DS5-67 was the first improved germplasm line derived from PI 462312. DS31-243 was the first improved germplasm line with resistance to mature seed damage caused by heat, mold, stink bugs, weathering, etc. All three germplasms contributed to the diversification of the international gene pool of soybean. Seed of LG01-4561-14 were provided to the University of Hohenheim (State Plant Breeding Institute) in Germany to broaden their soybean breeding gene pool with exotic germplasm (PI 445837) and to the National Bureau of Plant Genetic Resources in India. DS5-67 was provided to the Paraguayan Institute of Agricultural Technology for developing rust-resistant cultivars. DS31-243 was provided to multiple U.S. university breeding programs (University of Missouri, University of Tennessee, and University of Arkansas) for developing cultivars with tolerance to mature seed damage and to Louisiana State University as a frog eye leaf spot-resistant check and parent for a genetic study. DS31-243, along with DS25-1, is currently (July 2023) being provided to the University of Agriculture in Faisalabad, Pakistan for heat tolerance screening and breeding. Released germplasm lines DB04-10836, DB0638-70, CM422, DS-880, and DS25-1, with high yield and resistance/tolerance to nematodes, rust, and heat, were transferred to the International Institute of Tropical Agriculture in Ibadan, Nigeria for Pan African Soybean Variety Trials. USDA-N6004, USDA-N6005 and USDA-N7005, in collaboration with this project, were released during the project period, each making significant advances to broaden the genetic base and yield potential of soybean germplasm in North American breeding programs. Multiple improved unreleased breeding lines and populations with traits of interest (yield, heat tolerance, drought tolerance, tolerance to mature seed damage and Phomopsis seed decay (PSD), and resistance to frog eye leaf spot) were transferred to public breeding and research programs (University of Arkansas, University of Missouri, Auburn University, University of Tennessee, Clemson University, North Dakota State University, and Louisiana State University) for multiple purposes (breeding improved cultivars, genetic studies, physiology/agronomy studies, MAGIC population development) during this project plan: LG11-8169-007F, DS34-1, DS1169-333, DS1169-122, DS1260-2, DS49-142, 11069-323-11, 11030-541-28, DS65-1, 14119-211-10, 11043-225-72, DB06x0006-93, DS1627-12, 11018-115-22, 11018-38-52, 11018-38-55, 11018-115-12, 11018-102-23, 11018-38-51, 11018-102-22, 11018-411-01, 11018-38-44, and 3 mapping populations. Also, soybean lines with high yield potential, elevated protein, low linolenic acid, diverse pedigree, stem canker resistance, nematode resistance, and/or tolerance to mature seed damage (including DA1037-25F, DA10x30-09F, DA10x30-48F, DA1134-015F, DA1242-01, DA13062-001F, DA13076-042F, DA13086-011F, DA13092-015F, DA13092-039F, DA13099-008F, DA1488-0228F, DA1539-109F, and DA1541-102F) were transferred to public breeding programs in Arkansas, Georgia, Kansas, Missouri and Tennessee as parents. These materials contributed to published research in refereed journals and to ongoing research and cultivar development. Five high oleic lines were transferred to an ARS lab in Maricopa, Arizona for inclusion in a genome wide association study to identify causes for variation in fatty acid composition and oil levels. Critical assays for rust resistance were conducted in house to fine tune our understanding of the inheritance of rust resistance and for the development of “pyramided” resistance genes from multiple sources. The use and maintenance of the project rust isolate collection was critical for determining which genes were involved. The Stoneville, Mississippi project developed a rapid cut-seedling inoculation method for PSD. Although PSD is a mature seed disease, this assay can be conducted at the seedling stage, with identification of PSD-resistant genotypes comparable to results from field tests of mature seeds. The cut-seedling inoculation technique can be used for the rapid evaluation of populations segregating for PSD resistance to identify new genes, as well as for high throughput phenotyping of PSD at the seedling stage for developing resistant cultivars. The project assayed the parents, F1 plants, and reciprocal F2 populations derived from two MG V parents in a field assay with overhead irrigation and artificial inoculation of plants. However, environmental variability among parents and checks was so great that we were unable to precisely phenotype these populations. We then followed our contingency plan, which was to develop genetic populations that could be replicated in time and space (unlike F2 populations), creating multiple segregating recombinant inbred line (RIL) populations to be assayed and mapped in the upcoming project. A recombinant inbred line (RIL) population was characterized for three field seasons (2017-2019) at Stoneville. Preliminary analyses identified significant associations between multiple genomic regions and multiple seed traits, including visual mold (fungal growth), purple seed stain, accelerated aging germination, hard seed, seed wrinkling, and green seed damage. The preliminary marker analyses were conducted before the retirement of the project’s molecular geneticist in December 2021. Based on these preliminary analyses for visual mold and purple seed stain, it was apparent that this population was likely also segregating for reaction to PSD. Hence, the information and materials gained from this study will carry over into the next project plan. During the field experiments, seed of the RIL population was characterized for multiple seed constituents, including total protein, individual amino acids (aspartic acid, threonine, serine, glutamic acid, proline, glycine, alanine, cysteine, valine, methionine, isoleucine, leucine, tyrosine, phenylalanine, lysine, histidine, arginine, and tryptophan), total oil, and carbohydrates (sucrose, raffinose, and stachyose). Preliminary mapping of each of the above traits was conducted. Germplasm accessions were maintained, increased, purified (including genomic testing), and the seed returned to the working collection in Urbana, Illinois for storage and distribution. The soybean collection was heavily used by both domestic and foreign scientists during the period of the project plan. In 2022 alone, 19,163 seed packets were distributed in the United States and to 20 other countries. This involved 11,679 accessions from 434 requests, which is over half (22,660) of the total number of accessions in the collection. This high demand indicates the international and domestic value of the collection. The Uniform Tests were grown, data collected, analyzed, and summarized, and reports published annually and distributed to customers. The Uniform Test is utilized by all public soybean breeders in the southern U.S.A. to obtain high-quality multi-location data to justify releases of their cultivars and germplasms. These public cultivars are not only grown by farmers, but are also shared among private and public breeding programs to improve future cultivars. In addition, public programs have worked for decades to increase the genetic diversity of U.S soybeans, which is important for continuing to make gain from selection. For example, data were used to release five high oleic acid lines from the University of Missouri from 2019-2021, which directly contributed to the United Soybean Board’s goals of increasing the production of high oleic soybean and of increasing the market share of soybean oil. The Stoneville program is responsible for organizing the tests, and for all seed distribution, data collection, statistical analyses, and report production. Stoneville performs all facets of the stem canker nursery. Parentage data for entries are now available in a searchable database at Soybase.org (2015-present). The Soybean Parentage database on Soybase.org was accessed 5529 times since 2016 by scientists, intellectual property departments of universities, and the U.S Patent and Trademark office (USPTO), among others. The USPTO accesses it multiple times yearly. Due to continual improvements during the five-year project plan, public soybean breeders now have more data, more usable data, higher quality data, raw data, and a visually improved annual report to use to make decisions and support releases. Increased funding was obtained to support Uniform Test collaborators who screen soybean lines for nematode resistance and seed composition traits. Dicamba has damaged our trials for the past 5 years, but the damage has steadily increased in the last 3 years. In 2022, the Mississippi State Official Variety Trial program grew 7 Uniform Test trials, but they were abandoned due to Dicamba damage and low rainfall. We have adapted by using non-Dicamba tolerant checks, as conventional soybean lines susceptible to Dicamba are frequently at a disadvantage when compared to Dicamba tolerant checks.


Accomplishments
1. The first food soybean seed quality evaluations in the southern United States (U.S.). Edamame is soybean that is harvested for consumption when immature and still green. The market for edamame in the U.S. is growing, but most edamame consumed in the U.S currently comes from China. ARS researchers in Stoneville, Mississippi, evaluated edamame breeding lines from three public breeding programs for quality and consumer taste preference. These evaluations were the first of their kind in the southern U.S. and contributed to the publication of the first information on quality and consumer taste perception of edamame breeding lines in the southern U.S. The sensory evaluation data were used to release edamame cultivar ‘VT-Sweet’ by Virginia Tech. The sensory evaluation of the edamame publication was cited eight times since 2021 and is guiding future development of cultivars. The registration article for VT-Sweet won an award for being one of the most highly cited articles in the Journal of Plant Registrations in 2021-2022.

2. The association of seed sugars and susceptibility to charcoal rot in soybean and its potential use as a biomarker in selection. Charcoal rot is a major disease of soybean that causes significant yield loss and poor seed quality. Currently, there are no resistant soybean cultivars available to growers, and the physiological and genetic defense mechanisms controlling this disease are unknown. The objective of this research was to investigate the role and responses of seed sugars in soybean genotypes that are moderately resistant (MR) and susceptible (S) to charcoal rot. ARS researchers in Jackson, Tennessee, and Stoneville, Mississippi, conducted a two-year field experiment under irrigated (IR) and non-irrigated (NIR) conditions in Jackson, Tennessee. The results showed that both MR and S genotypes had a wide range of sugar levels, but the MR genotypes had the ability to maintain higher levels of sucrose, glucose, and fructose (desirable sugars for taste and flavor) under the more severe NIR conditions. However, the S genotypes generally showed higher levels of stachyose (undesirable and considered anti-nutritional, causing flatulence in monogastric animals) and lower levels of sucrose, glucose, and fructose under both IR and NIR conditions. These associations may indicate a possible role of these sugars in a defense mechanism of soybean against charcoal rot, which suggests their potential use by breeders as biochemical markers for selecting genotypes with resistance to charcoal rot.


Review Publications
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.
 Shannon, G., Chen, P., Lee, Y.C., Vieira, C.C., Nascimento, E.F., Granja, M.O., Lee, D., Ali, M.L., Scaboo, A., Crisel, M., Smothers, S., Clubb, M., Nguyen, H.T., Li, Z., Mitchum, M.G., Bond, J., Meinhardt, C., Usovsky, M., Robbins, R.T., Gillen, A.M. 2023. Registration of ‘S11-17025C’ soybean: A high-yielding and high-oil conventional cultivar with broad resistance to diseases and nematodes. Journal of Plant Registrations. 17(2):329-342. https://doi.org/10.1002/plr2.20278.
 Fett, R., Gillen, A.M., Read, Q.D., Patel, S., Koebernick, J. 2023. Evaluating the accuracy and efficiency of test weight instruments for soybean (Glycine max L.) research. Agrosystems, Geosciences & Environment. 6:1-8. https://doi.org/10.1002/agg2.20354.
 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.
 Li, S., Smith, J.R. 2023. Phenotypic evaluation of soybean genotypes for their reaction to a Mississippi isolate of Phakopsora pachyrhizi causing soybean rust. Plants. 12-1797:1-14. https://doi.org/10.3390/plants12091797.
 Chamarthi, S., Kaler, A., Abdel-Haleem, H.A., Fritschi, F., Gillman, J.D., Ray, J.D., Smith, J.R., Purcell, L. 2022. Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean. The Plant Genome. 16(1). Article e20284. https://doi.org/10.1002/tpg2.20284.
 Li, S., Smith, J.R., Zhang, L. 2023. Evaluation of exotic soybean accessions and their use in developing improved soybean lines with resistance to Phomopsis seed decay. PLOS ONE. 18(6):e0286519. https://doi.org/10.1371/journal.pone.0286519.
 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.
 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., Ali, M.L., Shannon, G., Vieira,C.C., Lee, Y.-C., Nascimento, E.F., Granja, M.O., Lee, D., Crisel, M., Smothers, S., Clubb, M., Selves, S., Scaboo, A., Usovsky, M., Nguyen, H.T., Li, Z., Mitchum, M.G., Averitt, B., Bond, J., Meinhardt, C., Li,S., Gillen, A.M., Mengistu, A., Robbins, R.T., Mozzoni, L.A., Zhang, B., Smith, J.R., Moseley, D. 2023. Registration of ‘S16-5503GT’ soybean cultivar with high yield, broad adaptation, and glyphosate tolerance. Journal of Plant Registrations. 17:304-317. https://doi.org/10.1002/plr2.20269.
 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.
 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.