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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

2020 Annual Report

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.

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 falls under National Program 301, Component 1 (Crop Genetic Improvement) and Component 3 (Crop Biological and Molecular Processes) and focuses on development of improved soybean germplasm. The project has two research objectives and two research support objectives. In fiscal year 2020 (to date), the project’s research contributed to 19 peer-reviewed scientific publications, including the release of two germplasm lines. Research was conducted by ARS scientists and staff in Stoneville, Mississippi, with participation of collaborators from other institutions. This report summarizes the activities of the second year of the current five-year plan. 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. In this reporting period six high-yielding cultivars with broad disease resistance have been developed by university partners in collaboration with ARS Stoneville, Mississippi, researchers. Journal registration articles for four were published or in press and two more registration articles will be submitted soon. A total of 17 new advanced breeding lines were entered into the 2020 USDA Uniform Soybean Tests - Southern States (referred to herein as the Uniform Tests) along with four lines that were re-entered. Of the 17 new lines tested in 2020, nine were potentially heat-damage tolerant. Currently we have five advanced breeding lines that are ready to be released as soon as the release notices can be completed. These lines offer combinations of high yields, high seed protein content, improved tolerance to mature seed damage, and/or high seed quality. Additionally, one of the improved germplasm lines awaiting release has soybean rust resistance. Other breeding lines are at various stages of development and evaluation. The status and details of some of these potential germplasm releases are described below. In the 2019 maturity group (MG) 4-Late Uniform Test, two Stoneville lines ranked 1 and 6, respectively, for yield. Preliminary results indicate both lines have resistance to more than one species of nematode and had low levels of mature seed damage. They, along with six other advanced breeding lines, are in a reniform nematode-infested yield trial in 2020. One Stoneville line ranked number 1 for overall yield in 2018 and number 3 for yield in 2019 in the MG-5 Uniform Test. Three university programs have requested to use the line for breeding. In early Mississippi plantings, DS31-243 had higher yield and higher seed quality than similar-maturing commercial cultivars. Additionally, it has performed well in the Uniform Tests and is competitive for yield with commercial cultivars and has improved tolerance to mature seed damage over commercial cultivars. It is planned for release in 2021. The ongoing breeding for high oleic acid lines has now focused on incorporating the FAD2-1a_STOP allele into a locally adapted background. Other breeding work towards making unique high oleic acid and low linolenic acid breeding lines for further studies investigating the effects of environmental stresses on different gene combinations is on hold due to project limitations associated with the retirement of one of the project’s agronomists. Data analysis is continuing for the multiple years of Phomopsis data for near-isogenic lines that vary for seed oil oleic acid composition. In general, breeding continues towards developing lines with high yield potential, elevated protein and target oil levels with adaption to the midsouthern U.S.A., but greater emphasis is being placed on combining yield with reduced seed damage and resistance to Phomopsis seed decay. 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 resistance to Phomopsis seed decay, whereas Sub-objective 2B is focused on heat tolerance. However, there is overlap between the studies, as segregating populations developed for specific objectives were evaluated for multiple traits. Phomopsis seed decay is one of the most economically important soybean diseases. It results in poor seed quality in most soybean production areas in the world, especially in the mid-south region of the United States. Use of plant resistance is one of the most effective ways to manage the disease. The project’s pathologist evaluated 215 seed samples (1,075 plates) from multiple Phomopsis genetic populations developed by the project’s geneticists and the test results were provided to the geneticists. Analysis of the data is ongoing. Replicated seed plating assays for 67 advanced soybean breeding lines and checks from a Phomopsis field nursery is completed and analysis is ongoing. Additionally, concentrated Phomopsis spore suspension inoculum was prepared and provided to in-house soybean breeders developing resistance to Phomopsis seed decay and to public breeders at the University of Missouri. A three-year genetic study of 201 recombinant inbred lines was completed in 2019. Preliminary analysis identified quantitative trait loci (QTLs) associated with multiple traits related to seed quality, heat tolerance, mature seed damage, green seed damage, stink bug damage, Phomopsis seed decay and purple seed stain. Analysis is ongoing, and these data may contribute significant new information to the scientific community on the genetics of tolerance to seed damage traits. The same genetic population was utilized in 2018 and 2019 for seed composition phenotyping. Seed analysis for protein, oil, fatty acids, sugars, amino acids, and minerals has been completed, and data analyses are underway. Preliminary results indicate that seed composition differs among the lines, as well as between parents and controls. Conservation of available soybean genetic resources is the emphasis of Objective 3. Curation of the MG V-VIII portion of the USDA-ARS Soybean Germplasm Collection is an ongoing assignment. In the 2019 season, 1,105 accessions from the Assistant Curator were planted. Stands were good and routine line purification and morphological trait characterization were conducted in the field. Additionally, for a small number of accessions, leaf samples were taken, and DNA extracted, to determine the potential presence of the RR1 gene in the collection. In the fall of 2019, seed was harvested and over the winter cleaned mechanically and by hand. Cleaned seed from 2018 was returned to the collection at Urbana, Illinois. Cleaning seed from the 2019 harvest is ongoing (somewhat delayed due to the pandemic). In 2020, 578 four-row plots were planted for germplasm maintenance as well as 38 single rows of miscellaneous material, 38 two-row increases, 300 soja hills, and 46 hills for male-sterile screening, totaling 1,000 accessions (wild and domestic). In 2020, tissue samples are again being taken on a small number of accessions (28) for determining the presence of herbicide resistance transgenes in the collection. Objective 4 is focused on coordination of a regional testing program used by soybean breeders. ARS personnel in Stoneville, Mississippi, managed and coordinated the multi-location Uniform Soybean Tests – Southern States program, which is designed to evaluate new breeding lines for all Southern public soybean breeders. Data from the 2019 season were compiled and analyzed. The analyzed data was distributed to the participants on time; however, the pdf version of the final annual report was distributed July 7, 2020, and the hard copy has not been prepared as of early August 2020 due to personnel shortages and COVID-19 restrictions. The annual report summarizing the 2019 results was distributed to collaborators, participants, libraries and commercial breeders, and is available on the internet. Parentage data from the test were provided to the Soybean Parentage database at For the 2020 field season, seed was organized, packaged and distributed to cooperators. The 2020 trials at Stoneville were planted in a timely fashion and data collection is underway. Each year, in addition to overall coordination and management of the Uniform Soybean Tests, lines in the program are evaluated in a field experiment at Stoneville to measure their resistance to the fungal disease stem canker using inoculum prepared by the project’s pathologist. Results are included in the Uniform Tests annual report.

1. Identification of potential markers for selection of heat tolerance in soybean. High temperatures (30° C and above) limit soybean yields worldwide. Future climate projections indicate a potential for increased heat stress of food crops. DS25-1 was developed and publicly released in 2017 by ARS researchers in Stoneville, Mississippi, as the first improved heat-tolerant soybean, but its mechanisms for heat tolerance remain unknown. Saturated and mono-unsaturated fats are thought to play an important role in maintaining membrane stability in plant cells under heat stress. Growth chamber experiments producing heat stress were conducted on juvenile plants of DS25-1 and a heat-sensitive soybean line to determine relative levels of fats in leaf tissues subjected to heat stress. Heat-stressed field studies of mature plants were also conducted. DS25-1 had higher levels of saturated and monounsaturated fats, lower levels of polyunsaturated fats, and lower activities of the specific genes that code for polyunsaturated fats, indicating an association between heat tolerance and relative gene activity in DS25-1, versus the heat-sensitive line. This suggests that a decrease in polyunsaturated fats in DS25-1 promoted cell membrane stability and heat tolerance in DS25-1. Hence, reduced gene activity could be used as a potential marker by soybean breeders to develop heat tolerant soybean varieties for farmers. Researchers at Clemson University and ARS have increased their efforts to verify and expand these results. Clemson University posted this accomplishment on their website.

2. Identification of genes associated with drought tolerance in soybean. Drought is a major limitation to soybean yield and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency is associated with drought tolerance in plants. The objective of this study was to identify genes associated with water use efficiency. Water use efficiency was measured in a genetically segregating family of plants created and genotyped by ARS researchers in Stoneville, Mississippi. The 196-member family was screened in four field-environments by ARS and University collaborators (University of Arkansas and University of Missouri). Water use efficiency was determined to be highly heritable, with a total of 16 DNA regions on seven chromosomes found to be putatively associated with genes affecting water use efficiency. Molecular markers next to the identified chromosomal regions were described and may be used by soybean breeders to combine multiple desirable genes associated with drought tolerance into high-yielding soybean lines, thereby creating improved drought tolerant varieties for farmers.

3. The influence of agricultural practices, the environment, and cultivar differences on soybean seed protein, oil, sugars, and amino acids. Although seed composition constituents are genetically controlled, agricultural practices and environment significantly alter seed composition. Therefore, the objective of this study was to identify those factors that affect seed protein, oil, fatty acids, sugars, and amino acids. In a two-year field experiment, ARS researchers in Stoneville, Mississippi; Jackson, Tennessee; and researchers from the University of Tennessee were able to show that single or twin row with a seeding rate of 40,000 seeds per hectare resulted in higher protein, oleic, some sugars. However, a high seeding rate of 56,000 seeds per hectare resulted in lower protein, oleic acid, some sugars due to plant competition for soil nutrients, cultivar differences, and the yearly change of temperature. Application of nitrogen resulted in higher protein and linolenic acid. This research is beneficial to the scientific communities, including breeders and physiologists through advancing knowledge on the interactions between cultivars and environment for seed nutritional quality selection, and to soybean producers through consideration of best agricultural management to maintain high seed nutritional qualities.

4. Evaluation of soybean breeding lines for resistance to Phomopsis seed decay and for high seed germinability. Phomopsis seed decay is one of the most economically important soybean diseases in the midsouthern U.S.A. Identification of new sources of resistance and breeding soybean lines resistant to Phomopsis seed decay and that have high seed quality is one of most effective ways to control the disease. In this research, more than 200 breeding lines derived from parents with five sources of resistance and high seed quality were evaluated for percentage of Phomopsis seed infection and germination in Stoneville, Mississippi. Twenty-seven Phomposis seed decay-resistant homogeneous breeding lines with high seed quality were identified and tested in multi-year trials as a result of this project. Seed of seven improved soybean lines, 11043-225-72, 11043-224-91, 11030-541-28, 10061-236-11, 10076-121-11, DS65-1, and DS31-243, have been transferred to public and private soybean breeders for the purpose of developing high yielding varieties with less mature seed damage for Mississippi soybean producers. ARS researchers in Stoneville, Mississippi, expect this research will lead to the release of improved soybean lines with Phomposis seed decay resistance, high seed germinability, and lower seed damage. The new lines will reduce elevator dockage due to damaged seed and be capable of producing high quality seed beans.

Review Publications
Li, S., Sciumbato, G., Boykin, D., Shannon, G., Chen, P. 2019. Evaluation of soybean genotypes for reaction to natural field infection by Cercospora species causing purple seed stain. PLoS One. 14(10):e0222673.
Chen, P., Shannon, G., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C.C., Ali, L.M., Nguyen, H.T., Li, Z., Bond, J.P., Meinhardt, C.G., Klepadlo, M., Li, S., Mengistu, A., Robbins, R.T. 2020. Registration of ‘S14-15146GT’ soybean as a high-yielding RR1 cultivar with high oil content and broad disease resistance and adaptation. Journal of Plant Registrations. 14(1):35-42.
Narayanan, S., Zoong Lwe, Z.S., Gandhi, N., Welti, R., Fallen, B., Smith, J.R., Rustgi, S. 2020. Lipid metabolic changes contribute to heat tolerance in soybean. Plants. 9(4):1-17.
Bellaloui, N., McClure, A.M., Mengistu, A., Abbas, H.K. 2020. Influences of agricultural practices, environment, and cultivar differences on soybean seed protein, oil, sugars, and amino acids. Plants. 9(3),378.
Bazzer, S.K., Kaler, A.S., Ray, J.D., Smith, J.R., Fritschi, F.B., Purcell, L.C. 2020. Identification of quantitative trait loci for carbon isotope ratio in a recombinant inbred population of soybean. Theoretical and Applied Genetics.
Boehm Jr., J., Abdel-Haleem, H.A., Schapaugh Jr., W., Rainey, K., Pantalone, V.R., Shannon, G., Klein, J., Carter Jr, T.E., Cardinal, A.J., Shipe, E.R., Gillen, A.M., Chen, P., Smith, J.R., Weaver, D.B., Boerma, R., Li, Z. 2019. Genetic improvement of US soybean in maturity groups V, VI, and VII. Crop Science. 59(5):1838-1852.
Saha, S., Bellaloui, N., Jenkins, J.N., Mccarty Jr, J.C., Stelly, D.M. 2020. Effect of chromosome substitution from Gossypium barbadense L,G. tomentosum Nutt. Ex Seem and G. mustelinum Watt into G. hirsutum L. on cottonsend protein and oil content. Euphytica. 216:118.
Accinelli, C., Abbas, H.K., Bruno, V., Nissen, L., Vicari, A., Bellaloui, N., Little, N., Shier, W.T. 2020. Persistence in soil of microplastic films from ultra-thin compostable plastic bags and implications on Aspergillus flavus population. Waste Management. 113: 312-318.
Molin, W.T., Kronfol, R.R., Ray, J.D., Scheffler, B.E., Bryson, C.T. 2019. Genetic diversity among geographically separated Cyperus rotundus accessions based on RAPD markers and morphological characteristics. American Journal of Plant Sciences. 10:2034-2046.
Mengistu, A., Ray, J.D., Kelly, H.M., Lin, B., Yu, H., Smith, J.R., Arelli, P.R., Bellaloui, N. 2019. Pathotype grouping of Cercospora sojina isolates on soybean and their sensitivity to QoI fungicides. Plant Disease. 104:373-380.
Gillman, J.D., Biever, J.J., Ye, S., Spollen, W.G., Givan, S.A., Lyu, Z., Joshi, T., Smith, J.R., Fritschi, F.B. 2019. A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill. BMC Research Notes. 12:522.
Kaler, A., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Purcell, L.C. 2020. Genome-wide association mapping of dark green color index using a diverse panel of soybean accessions. Scientific Reports. 10.
Abbas, H.K., Bellaloui, N., Accinelli, C., Smith, J.R., Shier, W.T. 2019. Toxin production in soybean (Glycine max L.) plants with charcoal rot disease and by Macrophomina phaseolina, the fungus that causes the disease. Toxins. 11(11):645.
Chang, P.-K., Scharfenstein, L.L., Abbas, H.K., Bellaloui, N., Accinelli, C., Ebelhar, M.W. 2020. Prevalence of NRRL21882-like (Afla-Guard®) Aspergillus flavus on sesame seeds grown in research fields in the Mississippi Delta. Biocontrol Science and Technology.
Abbas, H.K., Bellaloui, N., Butler, A.M., Nelson, J.L., Abou-Karam, M., Shier, T.W. 2020. Phytotoxic responses of soybean (Glycine max L.) to Botryodiplodin, a toxin produced by the charcoal rot disease fungus, Macrophomina phaseolina. Toxins. 12(1):25.