Project : USDA ARS

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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

2021 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
ARS scientists at Raleigh, North Carolina, believe soybean is one of the least genetically diverse crops in the United States. 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). United States soybean breeders do not have the genetic resources in their programs to combat these problems and increase the sustainability and profitability of United States soy. Successfully meeting this challenge requires new genetic resources. Fortunately, the USDA-ARS is the main source of novel genetics for United States 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 continues to identify economically important genes and alleles preserved among the USDA SGC and transfer them into user-friendly germplasm, which are easily accessible to public and private sector scientists throughout the United States. ARS scientists at Raleigh, North Carolina research 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 United States soybean cultivars has dropped below a global standard of 48%. This undesirable marketing situation is the consequence of a decades-long decline in seed protein content in soybean. This decline 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 scientists 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 scientists 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 2021 ARS scientists at Raleigh, North Carolina authored or co-authored 10 publications demonstrating the value of Asian soybean and wild soybean as parental stock in applied soybean breeding. The unit grew over 60 acres of soybean to evaluate yield and produce new breeding lines. Scientists harvested more than 10000 yield plots and 5500 progeny rows of breeding lines developed from Asian or wild soybean accessions. More than 62 elite breeding lines from this research were entered in USDA Regional and the USB Regional Southern Diversity yield trials. PROGENY OF ASIAN SOYBEAN: ARS scientists advanced USDA germplasm from exotic soybean and it 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 2021, scientists are testing more than 4000 yield plots and 2000 progeny rows for development and evaluation of high-yielding high-protein United States adapted lines. One germplasm was released that included Asian soybean in their pedigree. One of these germplasm lines, provides a new source of yield-enhancing genes. PROGENY OF WILD SOYBEAN: A breeding pipeline has been developed to deliver agronomically valuable progeny derived from wild soybean in a set of plants that also deliver most of the genetic diversity and elevated seed protein in G. soja. Yield trial of fifteen such populations derived from genetically diverse wild parent are complete and the genomic analyses are underway. These progeny include individuals with yield comparable to the domestic parent and improved protein composition. Initial genomic analyses suggest that most of the genetic diversity of the wild parent can be captured in less than 10 progeny. ARS scientists have been leading a stakeholder funded “National Soybean Meal Protein” research team of 18 scientists from 12 major soybean growing states since 2017. ARS scientists at Raleigh, North Carolina are also investigating the impact of management practices, such as fertilization and tillage, on seed protein. In 2021, scientists have continued the preliminary field experiment for a Foundation for Food and Agriculture Research (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. 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 scientists 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 United States. 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 coordinated and led 10 scientists nationwide in a USB project on drought tolerance. To support this work, scientists grew more than 1000 yield plots and 1000 progeny rows of breeding lines developed from exotic drought-tolerant soybean in 2021. In addition, 116 commercial varieties were evaluated under drought to compare the level of drought tolerance exhibited in current, commercially available varieties to current breeding lines under development. Two breeding lines, N08-13890 and N11-10295, exhibit very low wilting scores, even under extreme drought conditions. N16-7526 also exhibits slow wilting under drought stress, but it is also resistant to ozone damage. ARS Raleigh, North Carolina is also a part of two grant-funded projects to screen soybean germplasm for heat stress tolerance and identify markers associated with heat tolerance. WINTER NURSERY: The Soybean Unit at ARS Raleigh, North Carolina also coordinates 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: Scientists from this unit led multiple national level grants funded by the United Soybean Board. The total grants received by the Unit in 2021 was more than $2.9 Million. An SY in the Unit is the principal investigator on a multinational multi-year FFAR grant. One graduate student, 4 postdoctoral fellows, six full time technicians and several part time workers were funded with extramural grants in 2021.

Accomplishments
1. Progeny derived by crossing wild and domesticated soybean improve genetic diversity and meal protein. ARS scientists at Raleigh, North Carolina, suggests the progeny of crosses between wild (G. soja) and domesticated (G. max) soybean often inherit poor agronomics traits like the vine-like growth habit and small black seeds of the wild parent. However, plants selected from large populations of progeny that inherit agronomically valuable traits from both parents can be identified. Individual biparental progeny have been identified by ARS researchers in Raleigh, North Carolina, that nearly equal the yield of the domesticated parent and produce higher meal protein levels of the wild parent. These breeding lines represent genetically novel resources for private and public breeders to improve both yield and seed protein of United States soybean cultivars.

2. Combined high-yield and high-protein in a MG-V breeding line with exotic pedigree. ARS scientists at Raleigh, North Carolina, believe United States soybean growers need cultivars that have both high yields and high proteins. ARS researchers have developed a MG-V line (N16-590) that has significantly higher protein with more than 100% seed yield when compared to the high yield check cultivars. This conventional line may be directly planted by the growers and be used by private and public breeders as a parent to improve protein without sacrificing yield. N16-590 can have far reaching impact, because 1% increase in meal protein without loss in yield may increase the value of United States soybean by $2 - 3 Billion. Majority of the soybeans grown in southeastern United States in 2021 belong to MG-V.

3. Release of a soybean germplasm line developed from soybean PI from Japan with high yield. ARS scientists at Raleigh, North Carolina, suggests the limited genetic diversity in United States soybean cultivars is well documented and continues to limit advances in soybean breeding. Modern soybean cultivars from Japan are genetically very distinct from United States cultivars and is an important source of diversity for applied breeding in the United States to create novel diversity. USDA-N7005 has a higher proportion of exotic germplasm (62.5%) in its pedigree than any other southern U.S. germplasm released in the past 40 years. This release exhibits superior yield and agronomic traits, as well as resistance to root knot nematode and stem canker. This new release is a desirable breeding stock for applied breeding.

4. Discovery of high protein, high yielding soybean mutant. ARS scientists at Raleigh, North Carolina, believe soybean is one of the most important and preferred sources of vegetable protein for animal feed. Developing high protein, high yielding soybean varieties is difficult due to the inverse relationship between yield and protein in soybean. Mutagenesis with gamma radiation converted an early maturity-group high yielding, high seed protein release from ARS researchers in Raleigh, North Carolina into a later maturing line with similar yield and seed protein. The mutagenized line derived from Holladay produced a line with high meal protein (>49%) and high yield (100% of low protein check cultivars).

5. Identified genotypic variation for heat stress response. ARS scientists at Raleigh, North Carolina, believe long-term elevated temperatures as well as short-term, intense heat waves can reduce photosynthesis and yield in soybean. Previous field studies have been restricted to a single soybean variety. In an open-air field experiment with six soybean varieties, ARS researchers increased the air temperature within plots by an average of +4.5°C during the seed fill period. Significant variability in temperature responses were observed among varieties. These effects could reduce soybean productivity and the value of soybean crop grown during unusually hot seasons. This screening method will allow identification of more heat tolerant varieties, which is critical in developing molecular markers associated with the trait.

6. Identified genotypic variation for carryover herbicide sensitivity. ARS scientists at Raleigh, North Carolina, suggest herbicide applied to rotational crops is expected to degrade before soybean is planted, but soil and environmental conditions may slow the degradation rate leading to unintended carryover herbicide that can damage a recently planted soybean crop. In a collaboration with NCSU, ARS researchers measured the carryover of atrazine in different North Carolina soil types. Five soybean varieties were exposed to atrazine concentrations that persist in soil. Of the five varieties, only one was unaffected by carryover of the herbicide. These data can help farmers select the best varieties to plant when carryover herbicide is suspected in their field due to weather conditions or soil type.

7. Identified novel sources of pest resistance in wild soybean. A search by ARS scientists at Raleigh, North Carolina, of the wild soybean germplasm collections in collaboration with researchers from North Carolina State University identified accessions that were resistant to guava root knot nematode (Meloidogyne enterolobii). The Guava root knot nematode is an emerging pest that threatens soybean yield in the United States. Two wild soybean accessions out of 65 tested have been identified with substantial resistance to this pest. These new genetic resources for pest resistance provide tools for soybean breeders to protect future soybean harvests from this important pest.

U.S. DEPARTMENT OF AGRICULTURE

Soybean and Nitrogen Fixation Research: Raleigh, NC