Research Project: Evaluation and Development of Improved Soybean Germplasm, Curation of USDA Accessions and Regional Evaluations of New Genotypes

Location: Crop Genetics Research

2019 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 2019, the project’s research contributed to 17 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 first 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. Seven new advanced breeding lines were entered, and eight lines were re-entered into the 2019 Uniform Soybean Tests, which is the last step before germplasm lines are selected to be formally released to breeders. Fatty acids are the primary components of vegetable oil. Research has shown that there are health benefits to consuming soybean oil with higher levels of oleic acid. Stoneville breeding programs are developing high oleic acid soybean lines with high yield potential and high germination potential. Some high oleic lines incorporate a new unique version of a gene that contributes to producing the increased level of oleic acid in these lines. Our first high oleic acid breeding line in regional tests had overall yield higher than the high oleic/low linolenic acid version of the check line ‘Ellis’. Work continues 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 to determine the optimal combination of genes for Mississippi. Breeding continues towards developing lines for the midsouthern USA with high yield potential and elevated protein with target oil levels. Evaluation and selection for multiple biotic and abiotic traits continues in the Stoneville soybean breeding program. Field experiments targeting breeding line seed composition and quality responses to abiotic stresses, including heat, are underway in 2019. Measurements include seed composition components protein, oil, fatty acids, sugars, amino acids, and other seed constituents as well as seed quality (germinability, seed damage, etc.). Breeding lines nearing release include breeding lines DA10x30-48F, LG11-8169-007F, and DA1134-015F. DA10x30-48F had the overall highest yield, second highest seed protein percentage, and achieved the industry target of 19% oil in the 2018 Uniform Test Maturity Group IV-Late Test. DA10x30-48F also has resistance to peanut root knot nematode, southern stem canker, and soybean cyst nematode HG type 5.7 (race 3). However, it is very susceptible to Phomopsis seed decay based on 2018 data from Jackson, Tennessee, and Stoneville, Mississippi. The genetically diverse breeding line LG11-8169-007F had yield similar to the appropriate checks, seed protein 1.9 to 2.2% higher than the checks, and was resistant to southern stem canker in the 2018 Uniform Test Maturity Group IV-Early Test. This line was selected from a population developed by an ARS scientist in Illinois and is also very susceptible to Phomopsis seed decay based on 2018 data. DA1134-015F ranked number one for overall yield in the 2018 Uniform Test Maturity Group V Test and is resistant to stem canker. It has acceptable seed protein and oil. Additionally, breeding line LG03-4561-14 was released (Docket Number 0057.18) as a novel, genetically diverse, high-yielding MG III soybean germplasm line for the early soybean production system in the midsouthern USA. New breeding lines have been developed and are being tested regionally and locally for yield, seed composition, Phomopsis resistance, nematode resistance, seed damage, and heat tolerance. Preliminary analysis of 2018 data shows that these breeding lines have as good or better Phomopsis resistance and less seed damage than check cultivars. Breeding lines will be further tested in coming seasons. For the 2019 field season, breeding lines were planted and stands looked good. Crossing nurseries were planted and the crossing programs initiated. 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. In the 2018 field season, populations segregating for Phomopsis resistance (PI 417050 x PI 597413 and PI 597413 x PI 417050) were grown in an established Phomopsis field nursery at Stoneville, inoculated with an isolate of P. longicolla, delay-harvested, and the harvested seed assayed for Phomopsis reaction. Seed plating assays are in progress for the populations. Another population (PI 424324B x 5601T) segregating for Phomopsis resistance was evaluated in greenhouse and growth chambers. For all segregating populations, tissue from each plant was sampled and DNA extracted so that the disease reactions can be associated and mapped with DNA markers. Sub-objective 2B is focused on heat tolerance and includes studies to identify genes associated with this trait and studies to investigate the effect of heat stress on seed composition and quality. An F6-deirved segregating population (DS25-1 x DT97-4290) consisting of 201 lines was grown at Stoneville in 2018, and the seed harvested in the fall for composition analysis and heat tolerance determinations. The population was previously analyzed with molecular markers. Phenotypic data collected for composition, heat tolerance, maturity, stem termination, flower color, and pubescence color will be associated with molecular markers and a map constructed. Quantitative trait loci for heat tolerance may be identified and associated with seed composition traits. A new stem termination gene may be identified. All new traits will be mapped as well as previously known locations of flower and pubescence color. In April 2019, the same population was planted in Stoneville for a second year of testing. 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 2018 season 1,021 accessions (domesticated and wild) were grown at Stoneville, Mississippi. The accessions were grown in 855 four-row plots and 99 two-row plots for seed maintenance and purification. Additionally, 67 hill plots were grown for identification of a specific gene. Seed from the plots were harvested, processed and transported to the soybean working collection at Urbana, Illinois. For the 2019 season, 1,105 accessions from the Assistant Curator were planted. Stands are good and line purification and morphological trait characterization is underway. 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 which is designed to evaluate new breeding lines for all southern public soybean breeders. Data from the 2018 season was compiled and analyzed. The 200+-page annual report summarizing the 2018 results was produced, distributed to collaborators, participants, libraries and commercial breeders, and is available online at: http://www.ars.usda.gov/Main/docs.htm?docid=23815. Parentage data from the test were provided to the Soybean Parentage database at Soybase.org. For the 2019 field season, seed was organized, packaged and distributed to cooperators. The 2019 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 Test program, lines in the test are evaluated in a field experiment at Stoneville to measure their resistance to the fungal disease stem canker. Results are included in the Uniform Tests annual report.

Accomplishments
1. Development of an improved soybean cultivar. Current U.S. soybean cultivars are derived from a small and narrow set of ancestral parents, resulting in a potential genetic bottleneck for yield and for vulnerabilities to new or invasive diseases and/or abiotic stresses. A novel, genetically diverse, high-yielding MG III soybean germplasm line (LG03-4561-14) was released by USDA-ARS researchers at Stoneville, Mississippi, Urbana, Illinois, and Jackson, Tennessee. LG03-4561-14 was derived from 25% exotic parentage and is the first released improved soybean germplasm line with PI 445837 in its pedigree. LG03-4561-14 was registered in the Journal of Plant Registrations, with seed deposited for long-term storage at Ft. Collins, Colorado, and for maintenance and distribution at Urbana, Illinois. This germplasm is the first MG III germplasm derived from exotic sources and released for use in the early production system of the southern USA. Seed of LG03-4561-14 has been requested by soybean breeders internationally from Germany and India, and is being used domestically in the USA in multiple public soybean breeding programs.

2. Development of a seedling screening methodology. Phomopsis seed decay can cause both yield and seed quality losses under some harvest conditions. Qualitative measurements of the disease can be extremely time consuming and expensive. A seedling inoculation and evaluation method for rapid screening soybean for resistance to Phomopsis seed decay has been developed by USDA-ARS researchers at Stoneville, Mississippi. Although Phomopsis seed decay is a soybean seed disease, results from the cut-seedling inoculation assays were comparable to those obtained from field tests. This research could facilitate the identification of resistance to Phomopsis seed decay without waiting for an entire growing season to conduct the seed assay. The method has been adopted by public soybean breeders in Southern Illinois University and two pathology laboratories in China.

3. Drought effects on seed quality components. Drought is a major abiotic stress factor that affects soybean seed composition and understanding the effects are critical to maintaining seed quality. USDA-ARS researchers at Stoneville, Mississippi, and Mississippi State University, Mississippi State, Mississippi, were able to determine that seed protein, palmitic and linoleic acids, sucrose, raffinose, stachyose, nitrogen, phosphorus, potassium, and calcium significantly decreased whereas oil, stearic, oleic and linolenic acids, and some minerals, including iron, zinc, copper, and boron increased in response to soil moisture stress. The changes in seed composition constituents were due to changes in nutrient accumulation in seeds under drought conditions. This information indicates the necessity of maintaining adequate soil moisture during flowering and seed-fill stages to obtain a high nutritional value of soybean seeds. This information also advances our knowledge of the effects of drought and irrigation management on seed quality and nutrition, and is also beneficial to breeders making drought tolerance selection.

Review Publications
Akond, M., Liu, S., Yuan, J., Kantartzi, S.K., Meksem, K., Bellaloui, N., Lightfoot, D.A., Kassem, M.A. 2018. Detection of QTL underlying seed quality components in soybean [Glycine max (L.) Merr.]. Canadian Journal of Plant Science. 98:1-8. https://doi.org/10.1139/cjps-2017-0204.
Dhanapal, A., Ray, J.D., Smith, J.R., Purcell, L.C., Fritschi, F.B. 2018. Identification of novel genomic loci associated with soybean shoot tissue macro- and micro-nutrient concentrations. The Plant Genome. 11:710066. https://doi.org/10.3835/plantgenome2017.07.0066.
Kaler, A.S., Ray, J.D., Schapaugh, W.T., Asebedo, A.R., King, A., Gbur, E.E., Purcell, L.C. 2018. Association mapping identifies loci for canopy temperature under drought in diverse soybean genotypes. Euphytica. 214:135. https://doi.org/10.1007/s10681-018-2215-2.
Liu, S., Wang, X., Yin, X., Bellaloui, N., McClure, M., Mengistu, A. 2019. Soybean seed isoflavone respond differentially to phosphorus applications in low and high phosphorus soils. Nutrient Cycling in Agroecosystems. 113(3):217-230. https://doi.org/10.1007/s10705-019-09982-3.
Gillen, A.M., Mengistu, A., Arelli, P.R., Stetina, S.R., Bellaloui, N. 2018. Registration of soybean germplasm line DB0638-70 with high yield potential and diverse genetic background. Journal of Plant Registrations. 13:96-102. https://doi.org/10.3198/jpr2018.03.0016crg.
Nandula, V.K., Montgomery, G.B., Vennapusa, A.R., Jugulam, M., Giacomini, D.A., Ray, J.D., Bond, J.A., Steckel, L.E., Tranel, P.J. 2018. Glyphosate-resistant junglerice (Echinochloa colona) from Mississippi and Tennessee: Magnitude and resistance mechanisms. Weed Science. 66:603-610.
Mengistu, A., Kelly, H., Bellaloui, N., Arelli, P.R., Lin, B. 2018. Quantifying the effects of fungicides and tillage on Cercospora sojina severity and yield of soybean. Plant Health Progress. 19:226-232. https://doi.org/10.1094/PHP-04-18-0017-RS.
Deng, Y., Hsiang, T., Li, S., Lin, L., Wang, Q., Chen, Q., Xie, B., Ming, R. 2018. Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests short fragment insertions as a potential factor leading to larger genomic size. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.02079.
Li, S. 2018. Development of a seedling inoculation technique for rapid evaluation of soybean for resistance to Phomopsis longicolla under controlled conditions. Plant Methods. 14:81. https://doi.org/10.1186/s13007-018-0348-x.
Bellaloui, N., Abbas, H.K., Ebelhar, W.M., Mengistu, A., Mulvaney, M.J., Accinelli, C., Shier, T.W. 2018. Effect of increased nitrogen application rates and environment on protein, oil, fatty acids, and minerals in sesame (Sesamum indicum) seed grown under Mississippi Delta conditions. Food and Nutrition Sciences. 9:1112-1135. https://doi.org/10.4236/fns.2018.99081.
Wijewardana, C., Reddy, R., Bellaloui, N. 2018. Soybean seed physiology, quality, and chemical composition under soil moisture stress. Food Chemistry. 278:92-100. https://doi.org/10.1016/j.foodchem.2018.11.035.
Kaler, A., Bazzer, S., Sanz-Saez, A., Ray, J.D., Fritschi, F., Purcell, L. 2018. Carbon isotope ratio fractionation among plant tissues of soybean. The Plant Phenome Journal. 1:180002. https://doi.org/10.2135/tppj2018.04.0002.
Smith, J.R., Ray, J.D., Mengistu, A. 2018. Genotypic differences in yield loss of irrigated soybean attributable to charcoal rot. Journal of Crop Improvement. 32(6):781-800. https://doi.org/10.1080/15427528.2018.1516262.
Smith, J.R., Gillen, A.M., Nelson, R.L., Bruns, H.A., Mengistu, A., Li, S., Bellaloui, N. 2019. Registration of high-yielding exotically-derived soybean germplasm line LG03-4561-14. Journal of Plant Registrations. 13:237-244. https://doi.org/10.3198/jpr2018.09.0061crg.
Averitt, B., Zhang, B., Li, S., Chen, P. 2017. A survey of the agronomic and end-use characteristics of low phytic acid soybeans. In: Fletcher, B., editor. Soybeans: Cultivation, Nutritional Properties and Effects on Health. Hauppauge, NY: Nova Science Publishers, Inc. p. 21-33.
Cheng, Y., Ma, Q., Ren, H., Xia, Q., Song, E., Tan, Z., Li, S., Zhang, G., Nian, H. 2017. Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing. Theoretical and Applied Genetics. 130(5):1041-1051. https://doi.org/10.1007/S00122-017-2869-5.