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

2022 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 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 U.S. soy. Successfully meeting this challenge requires new genetic resources. 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. The Soybean and Nitrogen Fixation Research Unit (SNFRU) 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 U.S. 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 U.S. 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. 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. The SNFRU is 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. SNFRU seeks 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 farmers' fields. In 2022, we authored or co-authored 13 separate publications. The Unit grew over 70 acres of soybean to evaluate yield and produce new breeding lines. SNFRU harvested more than 8000 yield plots and 8000 progeny rows of breeding lines developed from crosses with unimproved Asian or wild soybean accessions. More than 50 elite breeding lines from this research were entered in USDA Regional and the USB Regional Southern Diversity yield trials. Research from 6070-21220-069-000D is entitled “Exploiting Genetic Diversity through Genomics, Plant Physiology, and Plant Breeding to Increase Competitiveness of U.S. Soybeans in Global Markets”. PROGENY OF EXOTIC ASIAN SOYBEAN: Our advanced USDA germplasm derived from unimproved PIs from the SGC 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 2022, we are testing more than 2500 yield plots and 3000 progeny rows for development and evaluation of high-yielding high-protein U.S. adapted lines. One germplasm (USDA-N7005) was released that included exotic Asian soybean in their pedigree and 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 and genetic marker analysis of fifteen such populations derived from genetically diverse wild plant are complete. Three hundred interspecific progeny have been identified that yield over 70% of the G. max parent and have valuable seed composition traits. Twenty-eight of these progeny yield between 90% and 101% of the G. max parent and often have elevated seed protein. For most populations over 90% of the genome of the wild parent has been captured in 6-10 agronomically valuable progeny. Our Unit leads the “National Soybean Meal” research team of 18 scientists from 12 major soybean growing states. We are also investigating the impact of management practices, such as fertilization and tillage, on seed protein. This study includes multiple genotypes to capture genetic diversity in responses of seed protein to farm management. In 2021, we have continued the preliminary field experiment for a FFAR-funded project to protect soybean protein production and stability under 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. We 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. This Unit coordinated and led over 10 scientists nationwide in a USB project on drought tolerance. To support this work, the unit grew more than 1000 yield plots and 1000 progeny rows of breeding lines developed from exotic drought-tolerant soybean in 2022. 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. We evaluated the link between drought tolerance strategies and seed composition responses to drought in twelve soybean genotypes under irrigated and rainfed conditions in the field. Our first year of data indicates that a slow wilting-high protein line is better able to maintain leaf water potential across a range of soil moisture values than other genotypes. This Unit led a collaboration with scientists in the U.S. and Belgium to measure genotypic variation in heat stress responses. Ten soybean genotypes were grown in custom built, open-air heated field plots. We measured variation among genotypes in physiological responses and in the responses of yield and seed oil concentration to elevated temperatures during seed fill, and we found genotypic variation in nighttime respiration rates, photosynthetic capacity, and seed oil concentration in plants grown at elevated temperature. Analysis of the heat stress phosphoproteome is ongoing. WINTER NURSERY: The Soybean Unit 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 lead nationally coordinated grants from the United Soybean Board. One of the SYs in this unit is the principal investigator on a multinational multi-year FFAR grant. One graduate student, four full time term technicians and 4 postdoctoral fellows were funded on extramural grants.

Accomplishments
1. Identified several genes and biological processes that underlay the mechanism behind the slow wilting trait of PI 471938. PI 471938 was originally identified as a drought tolerant soybean genotype by ARS researchers in Raleigh, North Carolina, in the early 2000s and it delays wilting in response to a water deficit. Since then, this genotype has been used in many breeding programs to develop drought tolerant cultivars. Despite its extensive use, the mechanism responsible for its slow wilting response under drought stress is still largely unknown. A total of 44,934 differentially expressed genes (DEGs) were initially identified between the elite parent NC-Roy (drought susceptible) and PI 471938 under well-watered vs drought-stressed treatments. Several DEG’s were related to water stress, respiratory electron transport, aerobic respiration, and heat shock. Identification of these genes leads to a better understanding of the mechanism behind PI 471938’s slow-wilting trait. This information will lead to future advancements in improving drought tolerance in soybean.

2. Identified variation in high temperature responses among soybean varieties. Climate change is increasing average temperatures during the growing season. High temperatures can adversely affect soybean yield and quality. ARS researchers in Raleigh, North Carolina, identified genetic resources to improve soybean heat stress tolerance. We measured the high temperature response of several soybean varieties in fields using custom-built, open-air chambers that elevate the air temperature by 4.5°C above the ambient. The elevated temperature treatment increased nighttime respiration and reduced seed oil concentration across varieties. The soybean varieties had different temperature responses for seed protein concentration as well as some photosynthetic and water use parameters. These results show that soybean heat stress responses could be improved through breeding to mitigate the effects of climate change and that seed oil concentration could be an area of concern in future climate conditions. The results from this study were published in a peer-reviewed journal, and future studies will explore these heat responses more in-depth.

3. Developed a high oil high yielding soybean line with flood tolerance. Soybean oil is widely used in both industrial and food sectors and accounts for up to 40% of the value of the U.S. soybean crop. Flood stress at critical growth stages can reduce soybean yield by as much as 27%. ARS researchers in Raleigh, North Carolina, have developed a high-yielding maturity group VI line (N11-352) with one of the highest oil contents among U.S. cultivars. N11-352 is also flood tolerant. Public release of this line as germplasm is currently underway. This novel germplasm with two economically important traits, high seed oil and flood tolerance, is valuable for improvement of these traits in the U.S. commercial cultivars and make them more profitable for growers.

4. Developed high-yielding high seed-protein lines from wild soybean crossed with domesticated soybean. Development of high yielding soybean lines from a cross with wild soybean is extremely challenging, because the progeny often inherit negative qualities from the wild parent, including viny growth habit, small seeds, and pods that are prone to shattering, which prevent machine harvesting necessary for modern agriculture. ARS scientists at Raleigh, North Carolina, used novel breeding methods to select progeny from such crosses to overcome these challenges. Twenty-eight progeny have been identified that yield between 90 % and 101 % of the domesticated parent. Many of these accessions have elevated levels of seed-protein as well. These progeny demonstrate the value of the USDA soybean germplasm collection to improve seed composition and genetic diversity of the U.S. soybean crop. These exceptional germplasm will be useful to public and private breeders working to improve the genetic diversity and seed protein content of U.S. commercial cultivars.

U.S. DEPARTMENT OF AGRICULTURE

Soybean and Nitrogen Fixation Research: Raleigh, NC