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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

2022 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
In fiscal year 2022 to date, the project’s research contributed to 20 peer-reviewed scientific publications, including the release of one germplasm line (DS31-243). Research was conducted by ARS researchers in Stoneville, Mississippi, with participation of collaborators from other institutions. Objective 1 of the project is to develop and release novel soybean germplasm that is well suited for sustainable production, especially in the southern USA. Eighteen breeding lines with maturities ranging from early IV to V were tested in the 2021 USDA Uniform Soybean Test—Southern States (referred to herein as the Uniform Tests). In the 2022 season, six new advanced breeding lines were entered into the Uniform Tests and eight lines were re-entered. The breeding lines have a range of traits including tolerance to mature seed damage, tolerance to heat and drought, and resistance to soybean cyst and reniform nematodes. Other breeding lines combining various traits are at different stages of development and evaluation. ARS researchers concluded four years (2018-2021) of combining and selecting for four drought tolerance traits in single plants, each having 50% of their background coming from the elite parent, LG11-8169-007F (developed by ARS researchers). Markers were employed after each cycle of selection to confirm true crosses. F2 plants and F2:3 families were grown in Mississippi in 2021, where both genomic and phenotypic selection were successfully employed to select the most agronomically elite plants with the most alleles associated with drought tolerance. In 2022, selected F2:3 and F3:4 families were planted in Mississippi for continued selection. Future homogeneous lines developed from these selections will be tested in combined irrigated/rain-fed trials, with the best drought-tolerant lines released. Across two years in 2020 and 2021, ARS scientists at Stoneville, Mississippi, designed and led a multi-state drought tolerance trial to compare two sets of sister lines developed by ARS researcher in Stoneville, Mississippi. One set of sister lines was selected to have high water-use efficiency (WUE) and the second set of sister lines was derived from the same parents but selected to have low WUE. In locations with adequate data and drought stress, lines with high water-use efficiency had the lowest yield loss under rain-fed production, relative to adjacent irrigated production, compared to the lines selected to have low WUE. One of the breeding lines with high WUE across both years was determined to also have heat tolerance in 2021 and entered into the 2022 Uniform Tests. Breeding lines resistant to reniform nematode, along with current cultivar checks of similar maturity, were yield tested on infested ground across two years in 2020-21, with reniform nematode counts taken at planting and at harvest. Reniform nematode-resistant breeding lines had higher yields than all cultivar checks and fostered the lowest reproduction of nematodes. The highest yielding of these reniform-resistant lines is in the 2022 Uniform Test. The Phomopsis/Mature seed decay (MSD) nursery was conducted in 2021 and had high levels of Phomopsis seed decay (PSD), but low levels of MSD. The pathologist provided a concentrated spore suspension of Phomopsis longicolla for making five gallons of working inoculum for the project PSD nursery. From the 2021 nursery, 158 soybean seed samples from 33 breeding lines and 20 checks were evaluated by seed plating assays. This field trial was inoculated with P. longicolla, experienced overhead watering each day, and each plot was harvested two weeks after maturity. Breeding lines in the trial were derived from multiple pedigrees and utilized at least six sources of PSD-resistance. The seed plating results from two 25-seed samples were provided to the breeders. Assays showed that there were significant differences (P = 0.05) in seed infection by P. longicolla among soybean lines, ranging from 18.7% (15097-225-21) to 100% (LG03-4561-14, susceptible check) among lines in the early-maturity test, while the range of Phomopsis seed infection was from 34.7% (10049-142-3) to 88.0% (AG 4632, susceptible check) among lines in the late maturity test. Hence, progress is being made on field screening for these traits. A 2021 PSD study used a set of Clark maturity isolines to evaluate the effect of maturity/weather on infection. The Clark isolines range in maturity from MG II to V. The data indicated that the timing of warm wet weather affected disease development and is therefore critical in determining disease and damage severity. Experiments were conducted to test the responses of eight ARS breeding lines (potentially containing genes Rpp4 or Rpp6) and seven high oleic entries from public breeders to soybean rust (SBR; Phakopsora pachyrhizi) isolates. The evaluation also included eight soybean accessions with known rust genes, plus susceptible and cultivar checks. Four breeding lines that had low severity and sporulation ratings in our tests were identified. In addition, as part of the National Plant Disease Recovery System-funded project, experiments were conducted to test and confirm the virulence of P. pachyrhizi isolates collected from Mississippi and other southern states from 2006 to 2016 with a panel of differentials containing Rpp genes (Rpp1 through Rpp7) and susceptible check Williams 82. In addition, the soybean pathologist in Stoneville, Mississippi, developed an improved protocol for maintaining P. pachyrhizi isolates on detached leaves under controlled conditions. Fifteen advanced breeding lines, with diverse SBR resistance confirmed by ARS scientists at Ft. Detrick, Maryland, were yield tested across two years (2020-2021) and were planted again in yield trials at Stoneville, MS in 2022. Previously, they were yield tested under high rust pressure in Paraguay. The lines were developed for the southern U.S. and will be released. The work supporting Objective 2 is designed to identify and characterize traits and genes influencing soybean plant health and physiology, including the development of breeder-friendly selection methodologies. Sub-objective 2A is focused on investigating resistance to PSD, whereas Sub-objective 2B is focused on investigating resistance to heat tolerance and other seed related traits. There is overlap between these sub-objectives, as segregating populations developed originally for 2B will be used in inheritance studies for both 2A and 2B. In 2021-22 for 2A, F2:3 genetic populations are being created and a recombinant inbred line (RIL) population (12060) is being increased and characterized for future assays. For 2B, preliminary data analysis from the three-year (2017-2019) field study of the 201-line RIL population (12047) tentatively identified major quantitative trait loci associated with seed damage, mold, and seed germination. The analyses in 2021 focused on the relationship between rainfall (amount and timing) and the various seed traits relative to maturity. Other analyses are on-going, and this study may contribute significant new information on the genetics of tolerance to seed damage caused by heat, mold, green seed, and wrinkling. Also, leaves taken from the 2019 planting were assayed in 2021 for macro- and micro-nutrients, including nitrogen, phosphorus, potassium, sulfur, calcium, magnesium, boron, copper, and zinc, and iron. This was to understand how levels of nutrients in the leaves are related to nutrient levels in the seed (previously assayed) and how these levels are related to heat tolerance and seed damage. RIL population 12060, consisting of 301 lines, was grown for the first time in 2020 and phenotyped for seed composition traits (protein, oil, fatty acids, sugars, amino acids) in 2021. Conservation of the USDA soybean germplasm collection is the emphasis of Objective 3. In the 2021 season, 423 four-row plots for germplasm maintenance, 168 single rows of miscellaneous material, and 200 Glycine soja (wild) hills were curated. Additionally, DNA was isolated from accessions with possible GMO contamination and molecular markers run on the DNA. Based on marker data, appropriate plants were saved for seed purification. Cleaned seed from the 2020 nursery was returned to the working collection at Urbana, Illinois, while cleaning seed from the 2021 harvest is ongoing. In 2022, 741 four-row maintenance plots were planted for germplasm maintenance, as well as 30 one-row plots of miscellaneous material, 100 G. soja hill plots, and 80 male sterile hills to classify. Objective 4 is focused on coordination of a regional testing program used by public soybean breeders. ARS personnel in Stoneville managed and coordinated the multi-location Uniform Tests, which is designed to evaluate new breeding lines for all Southern public soybean breeders. Data from the 2021 season were compiled, analyzed, and distributed to the participants on time, however very late arriving minor revisions to data have delayed publishing the final report. Each year, all lines (>300) in the program are evaluated in a field nursery at Stoneville for resistance to the fungal disease stem canker using inoculum (6,300 infested toothpicks) prepared by the project’s pathologist. The 2021 stem canker evaluation was successful. The project pathologist also provided 6,300 stem canker infested toothpicks to public soybean breeders for their breeding programs and collaborative research. The 2022 local trials and stem canker nursery were planted on time and are in progress.


Accomplishments
1. Development and release of improved MG IV soybean germplasm line with tolerance to mature seed damage. Mature seed damage, which includes, but is not limited to, visual mold, insect feeding, discoloration, and weathering, 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. There are currently no cultivars available to farmers that are tolerant to mature seed damage. ARS scientists in Stoneville, Mississippi, Jackson, Tennessee, and West Lafayette, Indiana, developed an improved MG IV soybean germplasm line that manifests significantly less seed damage, Phomopsis seed decay, and toxins from fungi than commercial cultivars, but also significantly higher seed germination than commercial cultivars. The new line, DS31-243, was competitive for seed yield in the southern early production system and was released by ARS in April 2022. 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 developing cultivars and will be deposited in the USDA soybean germplasm collection for use by scientists worldwide.

2. Development of high-yielding soybean cultivars with broad disease resistance through collaborative research with public soybean breeders and pathologists. There is a need for high-yielding cultivars with resistance to multiple diseases and abiotic stresses in the midsouthern U.S. ARS researchers in Stoneville, Mississippi, provided soybean disease inocula and technical support on disease assessments, and yield data, to a public soybean breeding program for the evaluation of soybean breeding lines for potential release as cultivars. As a result, eleven high-yielding cultivars (S13-2743C, S13-1955C, S13-3851C, S15-10434C, S13-10592C, ShowMeSoy 4301, S16-5540GT, S16-14730C, S16-15170C, S16-7922C, and S16-11651C) with broad disease resistance were registered in the Journal of Plant Registrations in FY22 by the University of Missouri. These are excellent cultivar choices for southern soybean growers and their publication will provide research information to both researchers and growers. The released cultivars are available to growers through The Missouri Foundation Seed Program.


Review Publications
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.
 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., 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., 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., 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., Shannon, G., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Ali, L.M., Lee, D., Lord, N., 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. ‘S16-14730C’: A high-yielding maturity group IV conventional soybean variety with indeterminate growth habit and multiple disease resistance adapted to the Mid-South. Journal of Plant Registrations. 16:287-299. https://doi.org/10.1002/plr2.20208.
 Chen, P., Shannon, G., Vieira, C., Ali, L.M., Lee, D., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Nguyen, H.T., Li, Z., Mitchum, M.G., Bond, J.P., Meinhard, C.G., Usovsky, M., Li, S., Gillen, A.M., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T., Moseley, D. 2022. Registration of ‘S16-15170C’ soybean: A high-yielding indeterminant maturity group V cultivar with wide adaptability and multiple disease resistance. Journal of Plant Registrations. 16:316-328. https://doi.org/10.1002/plr2.20220.
 Chen, P., Shannon, G., Lee, D., Vieira, C., Ali, L.M., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Nguyen, H.T., Li, Z., Mitchum, M.G., Bond, J.P., Meinhard, C., Usovsky, M., Li, S., Gillen, A.M., Mengistu, A., Zhang, B., Mozzoni, L.A., Robbins, R.T., Moseley, D. 2022. ‘S16-7922C’: A semi-determinate maturity group IV conventional soybean cultivar with high yield and broad disease resistance. Journal of Plant Registrations. 16:300-315. https://doi.org/10.1002/plr2.20211.
 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.
 Bellaloui, N., Mengistu, A., Smith, J.R., Abbas, H.K., Accinelli, C., Shier, T.W. 2021. Effects of charcoal rot on soybean seed composition in soybean genotypes that differ in charcoal rot resistance under irrigated and non-irrigated conditions. Plants. 10(9):1801. https://doi.org/10.3390/plants10091801.
 Knizia, D., Yuan, J., Bellaloui, N., Vuong, T., Betts, F., Register, T., Williams, E., Lakhssasi, N., Nguyen, H., Meksem, K., Mengistu, A., Kassem, M.A. 2021. The soybean high density Forrest by Williams 82 SNP-based genetic linkage map identifies QTL and candidate genes for seed isoflavones content. Plants. 10:1-23. https://doi.org/10.3390/plants10102029.
 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.
 Bellaloui, N., Abdelmajid, M.K. 2022. Seed protein, oil, fatty acids, and amino acids: effect of genetic and environmental factors. Springer Nature Applied Sciences. https://doi.org/10.1007/978-3-030-82906-3_1.
 Bagherzadi, L., Fallen, B.D., Gillen, A.M., Mcneece, B.T., Mian, R.M., Song, Q., Taliercio, E.W., Zenglu, L., Carter, T. 2022. Registration of USDA-N7005 soybean germplasm with high yield and 62.5% pedigree from Japanese accessions Tamahikari and PI 416937. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20209.
 Chamarthi, S.K., Kaler, A.S., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Dhanapal, A.P., King, C.A., Purcell, L.C. 2021. Identification and confirmation of loci associated with canopy wilting in soybean using genome wide association mapping. Frontiers in Plant Science. 12. Article 698116. https://doi.org/10.3389/fpls.2021.698116.
 Urrea, C.A., Smith, J.R., Porch, T.G. 2022. Registration of drought tolerant pinto SB-DT2 and small red SB-DT3 common bean germplasm from a shuttle breeding program between Nebraska and Puerto Rico. Journal of Plant Registrations. 16:400-409. https://doi.org/10.1002/plr2.20196.