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ARS Home » Southeast Area » Raleigh, North Carolina » Soybean and Nitrogen Fixation Research » Research » Research Project #434574
Research Project: Exploiting Genetic Diversity through Genomics, Plant Physiology, and Plant Breeding to Increase Competitiveness of U.S. Soybeans in Global Markets

Location: Soybean and Nitrogen Fixation Research

2020 Annual Report


Objectives
Objective 1: Use genomics, physiology and plant breeding approaches to identify novel genetic variation for various yield-enhancing traits in the USDA germplasm collection, transfer the traits to adapted backgrounds, and release germplasm or cultivars with improved yield potential. Sub-obj. 1a: Identify desirable genetic diversity for seed yield in exotic Asian soybean cultivars. Sub-obj. 1b: Identify desirable genetic diversity for improved seed yield in wild soybean. Sub-obj. 1c: Develop improved breeding methods and approaches for incorporation of genetic diversity from wild soybean to applied breeding programs. Sub-obj. 1d: Identify genomic differences between F1 hybrids and inbred parents that can be exploited as the basis for new breeding methodologies to augment existing applied breeding pipelines. Objective 2: Identify and characterize genetic variation for soybean oil and protein in the USDA germplasm collection, transfer the traits to adapted germplasm, and release improved germplasm or cultivars. Sub-obj. 2a: Elucidate physiological processes by which seed composition is improved without a yield penalty and connect these to the underlying genes. Sub-obj. 2b: Introgress desirable combinations of protein genes/QTL into MG V-VII high yielding conventional elite backgrounds. Sub-obj. 2c: Identify new genetic resources with high seed protein that lack the DBK high protein allele on chromosome 20 and identify QTL in those sources. Sub-obj. 2d: Determine if alterations of N metabolism and expression of asparagine synthase (AS) genes in vegetative tissues are associated with improved N content in progeny derived from the backcross of NMS4-44-329 to its parent N7103. Sub-obj. 2e: Determine if variation in a small RNA reported to regulate S uptake in Arabidopsis plays a similar role in soybean and characterize its mechanism of action. Sub-obj. 2f: Introgress desirable combinations of oil genes/QTL into MG V-VII high yielding conventional elite background to develop and release high performing germplasm with improved oil quantity and quality. Sub-obj. 2g: Combine high seed protein with drought tolerance in high yielding soybean backgrounds. Sub-obj. 2h: Improve soybean seed oil content and composition using wild soybean. Objective 3: Screen the USDA soybean germplasm collection to discover and elucidate traits governing genetic variation for molecular and physiological mechanisms that preserve yield under dry conditions, and use the information to develop and release soybeans with improved drought and heat tolerance. Sub-obj. 3a: Develop adapted drought tolerant breeding lines from exotic soybean germplasm. Sub-obj. 3b: Quantify the yield impact of the slow-wilting trait on yield in diverse environments. Sub-obj. 3c: Determine the impact of limited transpiration on leaf gas exchange and seed yield during drought. Sub-obj. 3d: Identify physiological and molecular traits that underlie successful nitrogen fixation response to drought. Sub-obj. 3e: Determine the ability of wild soybean accessions to germinate and grow at suboptimal temperatures and identify inheritance.


Approach
The USDA Soybean Germplasm Collection is one of the greatest biological resources in the world and a premier source of new genes for key soybean traits. Our team of experts genetically mines the Collection through breeding, genomics and plant physiology to provide novel customer-ready breeding stocks and production know-how to the soybean industry and society. The three objectives use wild and domesticated soybean germplasm from around the globe as a genetic basis for improving the yield potential and economic value of the U.S. soybean crop, while protecting crop production from the ravages of weather extremes, especially drought. A common approach in all three objectives is to blend cutting-edge field and lab research to transfer novel alleles and traits from the Collection into adapted, high-yielding, publicly-available USDA cultivars and breeding lines. Innovative plant breeding teams up with physiological and genomic research to make breeding advances and determine the mechanistic and molecular basis for them. These discoveries guide and refine future mining of the Collection, improving overall efficiency in utilizing the Collection and amplifying its impact. Because more than 90% of U.S. soybean acreage is grown in private varieties, private industry, rather than the public sector, will be the most immediate user of the novel USDA-ARS breeding stocks developed in this project. However, because all our products are non-GMO, they will also be used directly in the small but fast-growing conventional and organic soybean markets. To ensure the successful transfer of USDA products to the farm (either directly or more indirectly as breeding stock for private industry) it is essential that our USDA-ARS germplasm releases be ‘user ready’. In other words, germplasm released from the project must yield within 5% of current commercial cultivars, deliver stable traits and, when possible, include associated genetic markers. Integration of genomics, molecular biology and plant physiology with the top-notch ARS field breeding program makes this goal achievable.


Progress Report
Soybean is one of the least genetically diverse crops in the USA. As a result, this vital crop lacks the genetic capacity to resist emerging threats (such as new pests and increasing weather extremes) or adapt to new market demands (such as the high-protein soymeal market). U.S. soybean breeders do not have the genetic resources in their programs to breed solutions to combat these problems and increase the sustainability and profitability of US soy. Successfully meeting this challenge requires novel genetics. Fortunately, the USDA-ARS is the main source of novel genetics for U.S. soybean breeding. The USDA Soybean Germplasm Collection (SGC) includes over 20,000 domesticated (Glycine max) and wild (Glycine soja) accessions that represent most of the world’s diversity of soybean. ARS scientists at Raleigh, North Carolina, continue to identify economically important genes and alleles preserved among the USDA SGC and transfer them into user-friendly end products, which are easily accessible to public and private sector scientists throughout the United States. Research by ARS scientist at Raleigh, North Carolina, is accomplished through implementing state-of-the-art techniques in plant breeding, molecular genomics and plant physiology. Soybean meal (seed residue after oil extraction) is the world’s premier high-protein feed source for livestock, poultry and farmed fish, and it accounts for 60-70% of the total value of soybean. However, the protein content of meal produced from the majority of recently released commercial U.S. soybean cultivars has dropped below a global standard of 48%. This undesirable marketing situation is the consequence of a decade-long decline in seed protein content in soybean. A decline that has been attributed to a pervasive negative correlation between seed protein content and yield, which until recently was largely neglected. Additionally, soymeal is deficient in 5 important amino acids that must be added as supplements when the soymeal is fed to animals. ARS researchers at Raleigh, North Carolina, are addressing these problems by identifying and utilizing both wild and domesticated accessions as breeding stocks and by evaluating the role of agronomic practices in improving soy protein. ARS researchers at Raleigh, North Carolina, seek to enhance soybean competitiveness by using untapped genetic resources to improve seed composition and abiotic stress tolerance while maintaining yield comparable to the best yielding soybeans grown in farmer’s fields. In 2020, ARS researchers at Raleigh, North Carolina, authored or co-authored 7 publications demonstrating the value of Asian soybean and wild soybean as parental stock in applied soybean breeding. ARS researchers at Raleigh, North Carolina, grew over 99 acres of soybean to evaluate yield and produce new breeding lines. ARS researchers at Raleigh, North Carolina, harvested in excess of 12,000 yield plots and 10,000 progeny rows of breeding lines developed from exotic Asian or wild soybean accessions. More than 120 elite breeding lines from this research were entered in USDA Regional and the USB Regional Southern Diversity yield trials. PROGENY OF EXOTIC ASIAN SOYBEAN: ARS scientists at Raleigh, North Carolina, advanced USDA germplasm from exotic soybean is being used by public and private breeders to develop new cultivars with high yields and serve as checks in state and regional yield trials. In 2020, ARS researchers at Raleigh, North Carolina, tested more than 2000 yield plots and 5000 progeny rows for development and evaluation of high-yielding high-protein U.S. adapted lines. A total of 3 germplasm lines were released that included exotic Asian soybean in their pedigree. One of these germplasm lines, USDA-N6004, provides a new source of yield-enhancing genes. We have released a novel germplasm, USDA-N7004, with a rare combination of high (96%) yield of checks with high (49%) meal protein in 2019. In 2020, ARS researchers at Raleigh, North Carolina, have released an even better germplasm, USDA-N6005, with 100% yield of check cultivars and 49% meal protein. This germplasm also has 25% exotic diversity from Japanese cultivar Tamahikari. The release of this germplasm demonstrates the new genetic resources developed by ARS researchers at Raleigh, North Carolina, can overcome the negative correlation between protein and yield. PROGENY OF WILD SOYBEAN: A breeding pipeline has been developed by ARS researchers at Raleigh, North Carolina, to deliver agronomically valuable progeny derived from wild soybean in a set of plants that also deliver most of the genetic diversity in G. soja. Yield trials of three such populations derived from three genetically diverse wild plant introductions are complete and the genomic analyses is underway. ARS researchers at Raleigh, North Carolina, have developed agronomically-adapted progeny of wild soybean with an improved content of Sulfur-containing amino acids. Additionally, progeny with 25% wild soybean pedigrees that combine high protein and high yield are also in field trials in 2020. ARS researchers at Raleigh, North Carolina, also led the joint USB and FFAR funded “National Soybean Meal” research team of 18 scientists from 12 major soybean growing states. ARS researchers at Raleigh, North Carolina, are also investigating the impact of management practices, such as fertilization and tillage, on seed protein. For this study, ARS researchers at Raleigh, North Carolina, planted 144 plots. This study includes multiple genotypes to capture genetic diversity in responses of seed protein to farm management. In 2020, ARS researchers at Raleigh, North Carolina, have also begun the preliminary field experiment for a FFAR-funded project to protect soybean protein production from heat stress. This project has already annotated new soybean phosphatase genes which are of interest due to their potential role in heat stress signaling. IMPROVED OIL COMPOSITION: Worldwide, soybean is the most important oilseed crop (American Soybean Association, 2012). About 30%-40% of the value of soybean comes from its oil. Genetic improvement of soybean oil quantity, composition, and oxidative stability is needed for soybean to stay competitive in the global market. Populations derived from wild germplasm with higher amounts of oil and a higher percentage of saturated fats are in early stages of development. ARS researchers at Raleigh, North Carolina, are testing more than a 1000 yield plots and 2000 progeny rows to develop high-oil lines with high yield. DROUGHT and HEAT TOLERANCE: Late summer drought is the greatest yield barrier to soybean in the U.S. Heat stress is often overlooked in breeding programs, in part because symptoms of heat stress can be more subtle than those of drought stress. ARS researchers at Raleigh, North Carolina, coordinated and led over 10 scientists nationwide in a USB project on drought tolerance. To support this work, ARS researchers at Raleigh, North Carolina, grew in excess of 3000 yield plots and progeny rows of breeding lines developed from exotic drought-tolerant soybean in 2020. Visual rating of leaf wilting is currently a soybean breeders’ most effective tool for selecting drought tolerant soybean lines. ARS researchers at Raleigh, North Carolina, formed a collaboration with NCSU scientists to automate leaf wilting ratings in the field using computer vision and machine learning, with the initial trial resulting in approximately an 80% success rate for computer-evaluated leaf wilting images. In 2020, ARS researchers at Raleigh, North Carolina, have continued this trial with a greater number of soybean genotypes and updated technology in order to improve the computer’s accuracy. ARS researchers at Raleigh, North Carolina, also found, through analyzing three years of leaf gas exchange, soil moisture, and atmospheric data, that slow wilting genotype N06-9194 does not restrict water loss during dry conditions relative to fast-wilting NC Roy, despite descending from drought tolerant PI416937. WINTER NURSERY: ARS researchers at Raleigh, North Carolina, also coordinate the USDA-ARS soybean winter-nursery activities in Puerto Rico for all ARS soybean researchers, in collaboration with the USDA Research Unit in Mayaguez, Puerto Rico. As a result of this collaboration, the USDA soybean winter nursery had an outstanding winter season and higher-than-normal yields. GRANTS: ARS researchers at Raleigh, North Carolina, lead nationally coordinated grants from the United Soybean Board. An ARS researcher at Raleigh, North Carolina, is the principal investigator on a multinational multi-year FFAR grant. The North Carolina Soybean Producers Association provided funds to support two graduate students, who were mentored by ARS researchers at Raleigh, North Carolina,.


Accomplishments
1. Release of a new high-protein soybean germplasm with competitive yield and genetic diversity. The stakeholders are extremely concerned about the dipping of meal protein contents of recent U.S. soybean cultivars below the minimum market standard of 47.5%. To stay competitive in the international market, U.S. soybean growers and processors require high-yielding soybean with about 48% meal protein. ARS researchers at Raleigh, North Carolina, have recently released new germplasm, USDA-N6005, combining high (49%) meal protein and 100% yield of low protein check cultivars. It has 25% exotic pedigree derived from Japanese cultivar Tamahikari. This line will be a new resource for both public and private soybean breeders to develop high performing soybean cultivars with about 48% meal protein.

2. Received large grants from the United Soybean Board (USB). As soybean yields have increased in the US, the protein levels have decreased due to the historical negative correlation between protein and seed yield. The lower protein level puts U.S. soybean growers at a disadvantage in the international marketplace. The USB (the representative body of US soybean growers) have chosen ARS researchers at Raleigh, North Carolina, to lead two protein grants and one drought tolerance grant. ARS researchers at Raleigh, North Carolina, are also co-PI on a flood tolerance grant. One of these grants (jointly funded by FFAR) involves a large group of researchers from 12 states to remedy the negative effect on protein on seed yield. The USB has been funding us directly to the Unit and ARS researchers at Raleigh, North Carolina, are PI on grants since 2016 for execution of this research. With these additional grant supports, ARS researchers at Raleigh, North Carolina, have recently released two high yielding soybean germplasm with high meal protein. The second grant, which is led by an ARS researcher at Raleigh, North Carolina, involves collaborators in Florence, South Carolina, and it is aimed at optimizing agricultural management practices for seed protein concentration as well as understanding the underlying physiology.

3. Identified novel sources of pest resistance in wild soybean. A search of the wild soybean germplasm collections curated by ARS scientists at Raleigh, North Carolina, identified accessions that were resistant to soybean aphids or the soybean cyst nematode. Genomic analysis of the nematode resistance suggests that wild soybean has a different genetic basis for nematode resistance than the alleles currently deployed in elite soybean germplasm. Initial mapping of the aphid resistance indicates that the resistance can be inherited in progeny derived from a cross between wild and domesticated soybean. These new genetic resources for pest resistance provide tools to protect future soybean harvests from these important pests.

4. Identification of sulfur fertilization as a critical, previously overlooked factor in soybean seed protein concentration. Soybean meal protein concentration is largely determined by genetics, but the environment can also impact seed protein. Farmers can also use management practices to control some on-farm environmental factors, such as fertilization, tillage, and planting density or row spacing to impact seed protein content. ARS researchers at Raleigh, North Carolina, provided a meta-analysis of data from 64 previously published, peer-reviewed articles, and identified management practices that impact seed protein concentration. Nitrogen fertilization, tillage, irrigation, and row spacing decisions did not affect seed protein concentration across the meta-dataset. However, sulfur application significantly increased seed protein concentration, along with yield and seed oil concentration. This finding reveals that sulfur fertilization could be optimized to improve soybean seed protein concentration and that soybean sulfur metabolism should be a new focus area for soybean seed protein research. This research was chosen for an oral presentation at the 2019 CSA-ASA-SSSA annual meeting in San Antonio, Texas, and a manuscript describing this analysis and the results has been submitted for publication and is currently under peer review.

5. Advancements in slow wilting physiology and phenotyping. Breeders assess leaf wilting during periods without precipitation to identify potential drought tolerant soybean germplasm. ARS researchers at Raleigh, North Carolina, have discovered that hypothesized mechanism of limiting water loss during dry conditions has not been demonstrated in the field, and the exact conditions under which a slow wilting genotype might have an advantage or disadvantage had not been pinpointed. Over three years of soil moisture, atmospheric data, and diurnal measurements of leaf physiology, a slow-wilting genotype did not restrict stomatal conductance during dry conditions any more than the fast-wilting genotype, and it did not conserve soil moisture, indicating that stress tolerance mechanisms in the field might not be identical to those observed in chamber conditions Field-based research will be critical for validating mechanistic stress tolerance hypotheses. Additionally, ARS researchers at Raleigh, North Carolina, have collaborated with scientists at NCSU to develop an automated, remote system for leaf wilting ratings using computer vision and machine learning. Using low cost cameras mounted in the field, approximately 3000 images were manually rated for use as a training dataset. With ML algorithms, the computer was able to accurately rate images approximately 80% of the time. In 2020, ARS researchers at Raleigh, North Carolina, are continuing this project with updated cameras and more soybean genotypes to improve the training dataset.

6. Securing additional matching funds for a large competitive grant from the Foundation for Food and Agriculture Research (FFAR). The response of yield and protein production to temperature stress varies among soybean genotypes. Because this trait is difficult to assess in conventional breeding screens, ARS researchers at Raleigh, North Carolina, believe novel strategies are needed for selecting temperature stress-tolerant germplasm. FFAR and matching funders awarded funds to an SY in the Soybean and N Fixation Research Unit at Raleigh, North Carolina, to lead an international project that combines plant physiology, phosphoproteomics, and advanced machine learning-based modeling to discover new markers that can be used in soybean breeding. Matching funds (cash and in-kind) for this project were contributed by Benson Hill Biosystems, BASF, and the Flanders Institute for Biotechnology. In FY20, additional matching funds (cash) were secured for this project from the United Soybean Board and the North Carolina Soybean Producers’ Association. In the first year of this project, we have used bioinformatic analyses to identify new soybean phosphatases sequences, which will support our phosphoproteomics research.


Review Publications
Prenger, E.M., Mian, R.M., Buckley, B., Li, Z. 2019. Introgression of a high protein allele into an elite soybean variety results in a high-protein near-isogenic line with yield parity. Crop Science. 59:2498-2508.
 Singer, W., Zhang, B., Mian, R.M. 2019. Soybean amino acids in health, genetics, and evaluation. Intech. https://doi.org/10.5772/intechopen.89497.
 Lahiri, S., Reisig, D.D., Reay-Jones, F.P., Greene, J.K., Carter Jr, T.E., Mian, R.M., Fallen, B.D. 2020. Soybean host plant resistance to Megacopta cribraria (F.) (Hemiptera: Plataspidae) and the potential role of leaf trichome density. Environmental Entomology. XX(XX), 2020, 1–10. https://doi.org/10.1093/ee/nvz158.
 Ramos-Giraldo, P., Reberg-Horton, C., Locke, A.M., Mirsky, S.B., Lobaton, E. 2020. Drought stress detection using low-cost computer vision systems and machine learning techniques. IEEE IT Professional. https://doi.org/10.1109/MITP.2020.2986103.
 Taliercio, E.W., Scaboo, A., Baxter, I., Locke, A.M. 2019. The ionome of a genetically diverse set of wild soybean accessions. Crop Science. 59:1983-1991. https://doi.org/10.2135/cropsci2019.02.0079.
 Rosas-Anderson, P., Sinclair, T.R., Locke, A.M., Carter Jr, T.E., Rufty, T.W. 2020. Leaf gas exchange recovery of soybean from water-deficit stress. Journal of Crop Improvement. https://doi.org/10.1080/15427528.2020.1764429.
 Taliercio, E.W., Loveless, T.M. 2019. Identification of immunogenic epitopes of two soybean glycinin proteins in chicken. Food and Agricultural Immunology. 31:1, 75-83. https://doi.org/10.1080/09540105.2019.1700930.
 Robinson, K., Burton, J., Taliercio, E.W., Israel, D., Carter Jr, T.E. 2020. Inheritance of rhizobitoxine induced chlorosis in soybean. Crop Science. https://doi.org/10.1002/csc2.20193.
 Alam,R., Hummel, M., Yeung, E., Locke, A.M., Ignacio, J.I., Baltazar, M.D., Jia, Z., Ismail, A.M., Septiningsih, E.M., Bailey-Serres, J. 2020. Rice flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct. 4(7): 1-19. https://doi.org/10.1002/pld3.240
 Liu, L., Prenger, E.M., Zhang, J., Little, B., Mian, R.M., Li, Z. 2019. Impact of genotype, seed composition, agronomic trait and environment on soybean test weight. Journal of Crop Improvement. 33:6, 711-729. https://doi.org/10.1080/15427528.2019.1659205.
 Mcneece, B.T., Bagherzadi, L., Carter Jr, T.E., Mian, R.M. 2020. Registration of USDA-N7004 soybean germplasm with good yield, elevated seed protein and 25% exotic pedigree from Tamahikari. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20039.
 Lahiri, S., Reisig, D.D., Dean, L.L., Reay-Jones, F.P., Greene, J.K., Carter Jr, T.E., Mian, R.M., Fallen, B.D. 2020. Mechanisms of soybean host plant resistance against Megacopta cribraria (F.) (Hemiptera: Plataspidae). Environmental Entomology. https://doi.org/10.1093/ee/nvaa075.