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

Location: Crop Genetics Research

2021 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 2021 (to date), the project’s research contributed to 20 peer-reviewed scientific publications, including the release of one germplasm line. Research was conducted by ARS researchers in Stoneville, Mississippi, with participation of collaborators from other institutions. This report summarizes the activities of the third 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. All members of the team contributed expertise to various aspects of the breeding program, including breeding, genetics, disease screening, and seed composition determination. Seventeen breeding lines with maturities ranging from early IV to V were tested in the 2020 USDA Uniform Soybean Test—Southern States (referred to herein as the Uniform Tests). In the 2021 season, 10 new advanced breeding lines were entered into the Uniform Tests and 8 lines were re-entered. The breeding lines have a range of traits including tolerance to mature seed damage, tolerance to drought, and resistance to reniform nematode. Other breeding lines combining various traits are at different stages of development and evaluation. ARS researchers, working in collaboration with researchers at the University of Arkansas and the University of Missouri, concluded three years of combining four drought tolerance traits into single F1 seeds, 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. These F1 seeds were grown in an ARS greenhouse at Columbia, Missouri during the winter of 2020-2021, and the resulting F2 seeds were planted in Mississippi, Arizona, Arkansas, and Missouri, in spring 2021. Both genomic and phenotypic selection will be employed to select the most agronomically elite plants with the most alleles associated with drought tolerance. Future lines developed from these selections will be tested in combined irrigated/rain-fed trials, and the best lines released. In 2020, ARS researchers in Stoneville, Mississippi, designed and led a multi-state drought tolerance trial to compare two sets of sister lines developed by ARS scientists at Stoneville. One set of sister lines was selected to have high water-use efficiency and the second set of sister lines was derived from the same parents but selected to have low water-use efficiency. 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 water-use efficiency. These trials are being repeated in 2021 in Mississippi, Arizona, Arkansas, and Missouri. The breeding line with the highest seed yield and lowest yield loss under rain-fed production in 2020 was entered into the 2021 Uniform Tests. Breeding lines resistant to reniform nematode, along with current cultivar checks of similar maturity, were yield tested on infested ground in 2020, with reniform counts taken at planting and at harvest. Resistant breeding lines had higher yields than all cultivar checks and fostered the lowest reproduction of nematodes. This trial is being repeated in 2021 at Stoneville, Mississippi. Two of these reniform nematode-resistant breeding lines are in the 2021 Uniform Tests. Evaluation of breeding lines for resistance to mature seed damage and Phomopsis infection were carried out in furrow irrigated plots that were inoculated with a pure isolate of Phomopsis longicolla at the beginning of pod fill and then misted daily with water using overhead sprinklers. Two trials were conducted at Stoneville, Mississippi, with lines divided between trials based on maturity. The breeding lines were derived from multiple pedigrees and utilized at least six sources of Phomopsis resistance. Seed samples harvested from each line were evaluated by seed plating assays. Multiple breeding lines in both the early and late tests had significantly lower total damage scores and lower Phomopsis infection than those of susceptible checks for each trait. Two breeding lines with significantly lower mature seed damage and Phomopsis infection were entered into the 2021 Uniform Tests. Twenty-seven advanced breeding lines with putative rust resistance developed by this project were screened with 16 domestic and international isolates of Phakopsora pachyrhizi by ARS researchers in Ft. Detrick, Maryland. The evaluation also included 26 soybean accessions and check cultivars with known and unknown rust genes. The results indicated the previously unknown genetic source of resistance in 11 breeding lines and confirmed the source in another seven lines. At least three breeding lines with likely combinations of multiple resistance genes were identified as well as three lines with potentially new resistance genes. It is expected that multiple breeding lines with rust resistance 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 resistance to Phomopsis seed decay (PSD), whereas Sub-objective 2B is focused on heat tolerance and other seed related traits. However, there is overlap between the studies, as segregating populations developed for specific objectives were evaluated for multiple traits. Project scientists developed and executed a new seed plating protocol to evaluate seed diseases. The protocol is more efficient and eliminated the need for two individuals to work side-by-side. Among the non-breeding PSD studies in 2020, a set of Clark maturity isolines was tested to evaluate the effect of maturity/weather on infection. The Clark isolines range from MG II to V. All lines were delay-harvested from field trials inoculated with P. longicolla. The 2020 data are being analyzed and the study is being repeated in the 2021 season. A three-year (2017-2019) genetic field study of 201 recombinant inbred lines (RILs), two parents, and multiple checks was completed in fall 2019. Preliminary data for multiple traits related to seed quality, including heat tolerance and mature seed damage, tentatively identified major quantitative trait loci. The RIL population exhibited a wide range of maturities and the current analysis has focused on the relationship between rainfall (amount and timing) and 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 by heat, mold, green seed, and wrinkling. A second RIL population developed for heat tolerance was screened in 2020. The 301-member population was derived from a cross between DS34-1 (heat tolerant) and LD00-3309 (good yielder) and was screened for seed composition traits including protein, oil, fatty acids, sugars, and amino acids. Preliminary analysis indicated significant variability in these traits. This population is designed to be a confirming population for the seed quality/heat tolerance research. 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 2020 season, 578 four-row plots for germplasm maintenance, 38 single rows of miscellaneous material, 38 two-row increases, 300 Glycine soja hills, and 46 hills for male-sterile screening, totaling 1,000 accessions (wild and domestic) were planted. Stands were good and routine line purification and morphological trait characterization were conducted in the field. Additionally, leaf samples were collected from 19 accessions, DNA was isolated, and molecular markers run on the DNA to test for the presence of foreign genes. In the fall of 2020, seed was harvested and over the winter cleaned mechanically and by hand. Cleaned seed from 2019 was returned to the collection at Urbana, Illinois. Cleaning seed from the 2020 harvest is ongoing. In 2021, 423 four-row maintenance plots were planted for germplasm maintenance as well as 168 one and two-row plots of miscellaneous material, and 200 G. soja hill plots. Planting was timely and stands are good. Objective 4 is focused on coordination of a regional testing program used by public soybean breeders. Project personnel 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 2020 season were compiled, analyzed, and distributed to the participants on time, however very late arriving minor revisions to the protein and oil data have not been fully analyzed and distributed. The final 2020 annual report has not been completed and the 2020 pedigree data has not been given to the Parentage Database as of this writing due in part to a support scientist vacancy. The 2021 tests were distributed about a week late, but no planting was delayed. 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. The 2020 stem canker nursery was successful, and the 2021 nursery was planted on time and is in progress. Results are included in the Uniform Tests annual report.

Accomplishments
1. Effects of irrigation type and row-type on soybean seed nutritional qualities. Information on the effects of irrigation and row type (single versus twin) practices on soybean seed nutrition under the Southeast conditions is limited. Therefore, the objective of this research was to investigate the effects of irrigation and row-type on seed protein, oil, fatty acids, sugars, and amino acids. ARS researchers in Stoneville, Mississippi, conducted an experiment for two years in Stoneville, Mississippi, and found that most of these seed quality component were significantly affected by environment due to rainfall, heat, and solar radiation patterns, especially during July-August, coinciding with early reproductive and seed development stages. Seed protein and oil levels responded positively to irrigation, while most of the amino acids were not responsive. Amino acids, glycine, alanine, valine, and methionine levels were significantly higher in both full irrigation and alternate irrigation than rainfed irrigation. Seed sucrose was higher in rainfed irrigation than other irrigation types. Oleic acid was higher in rainfed irrigation, but no significant changes were observed in linoleic and linolenic acids. These results indicate that both irrigation and environmental factors, especially rainfall and heat during seed development can alter some seed composition constituents and play critical roles in determining seed nutritional qualities. Although environment played a key role in seed nutritional qualities, research results indicate a potential for improving soybean seed quality by managing irrigation.

2. Identification of a major-effect quantitative trait locus (QTL) for heat tolerance in soybean. Elevated temperatures during seed maturation can damage soybean seed by promoting seed wrinkling, green seed, and loss of vigor and viability. Future climate models predict increased potential for heat stress and damage of food crops. Breeding line 04030-1-4-1-1, derived from exotic soybean PI 587982A, was selected and developed by ARS researchers in Stoneville, Mississippi, to have high seed germinability under conditions of elevated temperatures. It was then used by ARS researchers in Columbia, Missouri, to create a 172-member genetic population for mapping traits. Emergence and germination were evaluated on the genetic population under heat stress conditions in six greenhouse and field environments at Stoneville and Columbia. A major novel QTL affecting tolerance to heat-induced degradation of soybean seed was identified. These findings greatly increase the possibility of using molecular markers to select for heat tolerance, thereby accelerating the development of heat tolerant cultivars for farmers worldwide. This information was disseminated by peer-reviewed publication and ARS scientists at Stoneville and Columbia have increased their efforts to fine map the genomic location of the QTL.

3. Evaluation of soybean breeding lines for resistance to Phomopsis seed decay and for high seed germinability. Phomopsis seed decay (PSD) is one of the most economically important soybean diseases in the midsouthern United States. Identification of new sources of resistance to PSD and breeding soybean for resistance to PSD with high seed quality is one of most effective ways to control the disease. ARS researchers in Stoneville, Mississippi, developed and executed a new seed plating protocol and eliminated the need for two individuals to work side-by-side. Seed samples harvested in 2019 and 2020 were evaluated by replicated seed plating assays for breeding lines and checks The breeding lines were derived from multiple pedigrees and utilized at least six sources of PSD-resistance. They were delay-harvested from field trials inoculated with Phomopsis longicolla. Results showed that there were significant differences in seed infection by P. longicolla among soybean lines, with some lines having as little as 4% infection (DA1239-09), while others had levels as high as 83% infection (cultivar LD00-7620). Twelve breeding lines had levels of infection less than 10%, which were all significantly less than the infection levels of susceptible checks. We expect this research will lead to the release of improved germplasm lines with PSD resistance, high seed germinability, and lower seed damage. The improved germplasm lines will be utilized in breeding programs to develop high-yielding cultivars that have reduced elevator dockage caused by damaged seed.

4. Evaluation of soybean breeding lines for resistance to Phomopsis seed decay and mature soybean seed damage. Phomopsis seed decay is one of the most economically important soybean diseases in the midsouthern United States. Damage to mature seed in the field is a significant economic problem when harvest is delayed due to rain. Identification of new breeding lines with resistance to Phomopsis and low levels of visible damage is a strategy to increase profits for farmers by reducing dockage at the grain elevator. Breeding lines derived from both PI sources of resistance and more traditional lines have been evaluated in an over-head irrigated nursery with delayed harvest for percentage of Phomopsis seed infection and percentage of mature seed damage. This year two soybeans lines, DA13099-008F and DA1488-0228F, which were bred primarily for yield, genetic diversity and SCN resistance, were shown to have low mature seed damage and moderate levels of Phomopsis in the nursery and good yield potential in the Uniform Tests. ARS researchers in Stoneville, Mississippi, transferred these lines by a material transfer agreement to the University of Missouri in 2020 and 2021, the University of Tennessee in 2021 and the University of Arkansas in 2021 for the purpose of developing high yielding lines with reduced mature seed damage and lower potential for dockage at the elevator for growers in the midsouthern United States.

5. Development and release of improved MG V germplasm line with resistance to soybean rust and Phytophthora root and stem rot. Soybean rust (SBR), caused by Phakopsora pachyrhizi, and Phytophthora root and stem rot (PRSR), caused by Phytophthora sojae, cause significant economic losses throughout the soybean-producing world. Genetic resistance to these fungal pathogens is environmentally friendly, non-GMO, and the lease expensive method for controlling these diseases. ARS researchers Stoneville, Mississippi, Ft. Detrick, Maryland, Urbana, Illinois, and West Lafayette, Indiana, developed an improved MG V soybean germplasm line that combined resistance genes Rpp3 and Rps1k for resistance to SBR and PRSR, respectively. The new line, DS5-67, was released by ARS in October 2020 and then transferred to soybean breeders for use in developing improved cultivars with resistance to these pathogens. DS5-67 will be especially useful for pyramiding (combining) multiple rust-resistance genes. It has been added to the USDA ARS Soybean Germplasm Collection as PI 698651.

Review Publications
Chen, P., Shannon, G., Crisel, M., Smothers, S.L., Clubb, M.W., Vieira, C.C., Ali, L.M., Selves, S.W., Lee, D.H., Scaboo, A.M., Klepadlo, M., Nguyen, H.T., Mitchum, M.G., Meinhardt, C.G., Bond, J.P., Robbins, R.T., Li, S., Smith, J.R., Mengistu, A. 2020. Registration of ‘S14-15138GT’ soybean as a high-yielding RR1/STS cultivar with broad disease resistance and adaptation. Journal of Plant Registrations. 14:311-317. https://doi.org/10.1002/plr2.20054.
Chen, P., Shannon, G., Ali, L.M., Scaboo, A.M., Crisel, M., Smothers, S.L., Clubb, M.W., Selves, S.W., Mitchum, M.G., Nguyen, H.T., Li, Z., Bond, J.P., Meinhardt, C.G., Klepadlo, M., Li, S., Mengistu, A., Robbins, R.T. 2020. Registration of ‘S14-9017GT’ soybean cultivar with high-yield, resistance to multiple diseases and high seed oil content. Journal of Plant Registrations. 14:347-356. https://doi.org/10.1002/plr2.20011.
Bellaloui, N., Saha, S., Tonos, J.L., Scheffler, J.A., Jenkins, J.N., McCarty Jr, J.C., Stelly, D.M. 2021. Effect of chromosome substitution from alien tetraploid cotton species in Upland cotton on (+) and (-) gossypol enantiomer levels in cottonseed. Journal of Cotton Science. 25:7-20.
Bazzer, S.K., Ray, J.D., Smith, J.R., Fritschi, F.B., Purcell, L.C. 2020. Mapping quantitative trait loci (QTL) for plant nitrogen isotope ratio in soybean. Euphytica. https://doi.org/10.1007/s10681-020-02726-3.
Li, S., Deng, Y. 2021. Mitochondrial genome resource of Phomopsis longicolla, a fungus causing Phomopsis seed decay in soybean. PhytoFrontiers. 1(2):120-122. https://doi.org/10.1094/PHYTOFR-10-20-0027-A.
Carneiro, R.C., Duncan, S.E., O'Keefe, S.F., Yu, D., Huang, H., Yin, Y., Neill, C.L., Zhang, B., Kuhar, T., Rideout, S., Reiter, M., Ross, J., Chen, P., Gillen, A.M. 2021. Utilizing consumer perception of Edamame to guide new variety development. Frontiers in Sustainable Food Systems. 4.556580. https://doi.org/10.3389/fsufs.2020.556580.
Bellaloui, N., Turley, R.B., Stetina, S.R. 2021. Cottonseed protein, oil, and minerals in cotton (Gossypium hirsutum L.) lines differing in curly leaf morphology. Plants. 10(3):525. https://doi.org/10.3390/plants10030525.
Bazzer, S.K., Kaler, A.S., King, C.A., Ray, J.D., Hwang, S., Purcell, L.C. 2020. Mapping and confirmation of quantitative trait loci (QTLs) associated with carbon isotope ratio (d13c) in soybean. Crop Science. 60:2479-2499. https://doi.org/10.1002/csc2.20240.
Nandula, V.K., Giacomini, D.A., Ray, J.D. 2020. Resistance to acetolactate synthase inhibitors is due to a TRP 574 to LEU amino acid substitution in the ALS gene of redroot pigweed and tall waterhemp from Mississippi. PLoS ONE. 15:6. https://doi.org/10.1371/journal.pone.0235394.
Bagherzadi, L., Gillen, A.M., Mcneece, B.T., Mian, R.M., and Carter Jr, T.E. 2020. Registration of USDA-N6004 Soybean Germplasm Derived from Japanese Cultivar Blue Side. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20064.
Chen, P., Shannon, G., Scaboo, A.M., Crisel, ., Smothers, S.L., Clubb, M.W., Selves, S.W., Vieira, C., Ali, L.M., Mitchum, M.G., Nguyen, H.T., Meinhardt, C.G., Klepadlo, M., Li, Z., Bond, J.P., Li, S., Smith, J.R., Gillen, A.M., Zhang, B., Mozzoni, L.A., Mengistu, A., Robbins, R.T. 2021. Registration of ‘S13-2743C’ as a conventional soybean cultivar with high oil content, broad disease resistance, and high-yield potential. Journal of Plant Registrations. 15:306-312. https://doi.org/10.1002/plr2.20081.
Huang, J., Ma, Q., Cai, Z., Xia, Q., Li, S., Chu, L., Lian, T., Nian, H., Cheng, Y. 2020. Identification and mapping of stable QTLs for seed oil and protein content in soybean [Glycine max (L.) Merr.]. Journal of Agricultural and Food Chemistry. 68:6448-6460. https://dx.doi.org/10.1021/acs.jafc.0c01271.
Krishnan, H.B., Kim, W., Oehrle, N.W., Smith, J.R., Gillman, J.D. 2020. Effect of heat stress on seed protein composition and ultrastructure of protein storage vacuoles in the cotyledonary parenchyma cells of soybean genotypes that are either tolerant or sensitive to elevated temperatures. International Journal of Molecular Sciences. 21(13). Article 4775. https://doi.org/10.3390/ijms21134775.
Gillman, J.D., Chebrolu, K., Smith, J.R. 2021. Quantitative trait locus mapping for resistance to heat-induced seed degradation and low seed phytic acid in soybean. Crop Science. 61(3):2023–2035. https://doi.org/10.1002/csc2.20419.
Mian, R.M., Mcneece, B.T., Gillen, A.M., Carter Jr, T.E., Bagherzadi, L. 2021. Registration of USDA-N6005 germplasm combining high yield, elevated protein and 25% pedigree from Japanese cultivar Tamahikari. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20139.
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., Meinhardt, C.G., Klepadlo, M., Li, S., Mengistu, A., Robbins, R.T. 2021. 'S13-1955C': A high-yielding conventional soybean with high oil content, multiple disease resistance, and broad adaptation. Journal of Plant Registrations. 15:318-325. https://doi.org/10.1002/plr2.20112.
Pinnamaneni, S.R., Anapalli, S.S., Sui, R., Bellaloui, N., Reddy, K.N. 2021. Effect of irrigation and planting geometry on cotton fiber quality and seed composition. Plants. 4(2):1-11. https://doi.org/10.1186/s42397-020-00078-w.
Stone, C.L., Smith, J.R., Ray, J.D., Gillen, A.M., Frederick, R.D. 2021. Phenotypic reactions of 53 soybean genotypes to infection with each of 16 isolates of Phakopsora pachyrhizi. Journal of Crop Improvement. https://doi.org/10.1080/15427528.2021.1904311.
Pinnamaneni, S.R., Anapalli, S.S., Bellaloui, N., Reddy, K.N. 2021. Effect of irrigation and planting geometry on soybean seed nutrition in humid climates. Crop, Forage & Turfgrass Management. 2021. Article 6625919. https://doi.org/10.1155/2021/6625919.
Bellaloui, N., Saha, S., Tonos, J.L., Scheffler, J.A., Jenkins, J.N., McCarty Jr, J.C., Stelly, D.M. 2021. Effects of interspecific chromosome substitution in upland cotton on cottonseed macronutrients. Plants. 10(6):1-13. https://doi.org/10.3390/plants10061158.