Project : USDA ARS

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

2019 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 among 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 increasingly common weather extremes) or adapt to new market demands (such as the high-protein soymeal market). Applied breeders do not have the genetic resources in their programs to breed solutions to these farm problems. Successfully meeting this challenge requires novel genetics. Fortunately, the USDA-ARS is the major source of novel genetics for U.S. soybean breeding. The USDA Soybean Germplasm Collection includes over 20,000 domesticated (Glycine max) and wild (G.soja) soybean types that represent most of the world’s diversity in soy. The Soybean Unit identifies economically important genes and alleles preserved among these USDA accessions and transfers them into user-friendly end products for the nation. Research is accomplished through state-of-the-art plant breeding, molecular and plant physiology approaches. YIELD IMPROVEMENT USING NOVEL GERMPLASM: In 2019, we authored or co-authored 10 publications demonstrating the value of exotic Asian soybean and wild soybean as parental stocks in applied breeding. The Unit grew over 85 acres of soybean to evaluate yield, harvested in excess of 17,000 yield plots and 5,000 progeny rows of breeding lines developed from exotic Asian or wild soybean. More than 100 elite breeding lines from this research were submitted to USDA regional trials and the USB Southern Diversity Regional yield trials. Exotic Asian Soybean: A total of 3 germplasms were released that included exotic Asian soybean in their pedigree. One of these germplasm, USDA-N6004, provides a new source of yield-enhancing genes for breeding. Our advanced USDA germplasm from exotic soybean is being used by public and private breeders to develop new cultivars which now top yield trials and serve as checks in state and regional yield evaluations. Wild Soybean: Our new germplasm release was featured on the cover of the May issue of Journal of Plant Registrations. The release and publication of these 17 lines derived from wild soybean is a milestone in soybean breeding because they transfer most of the genetic diversity of the wild soybean into agronomically valuable, breeder-friendly lines. A second generation of high yielding breeding lines, derived from these releases, are performing well in yield trials and are being considered for release. This research establishes that the wild soybean is an important source of genes to improve seed yield. SEED COMPOSITION IMPROVEMENT USING NOVEL GERMPLASM. High Protein: 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 soybean cultivars in the U.S. has dropped below a global standard of 48% to 46.5-47.5%. This undesirable marketing situation is the consequence of a decades-long decline in seed protein content in soybean resulting from intense breeder selection for high yield, a pervasive negative correlation between seed protein content and yield, and insufficient breeder attention to the developing protein problem. Additionally, soymeal is deficient in 5 important amino acids that must be added as supplements when the soymeal is fed to animals. ARS scientists are addressing this problem by identifying and utilizing both wild and domesticated germplasm as breeding stock and by evaluating the role of agronomic practices in improving soy protein. Wild Soybean: Evaluation of a representative cross section of the wild soybean germplasm collection has identified accessions with high seed protein and enhanced amino acid composition. ARS scientists are currently testing the heritability of these traits, their inter-relationship, and their effect on seed yield. Domesticated Soybean. In 2019, researchers are testing more than 2000 yield plots and 5000 progeny rows for development and evaluation of high-yielding high-protein U.S. adapted lines. ARS researchers have recently proposed the release of a novel germplasm, USDA-N7004, that demonstrates a rare combination of high yield with high protein. Several more of our advanced breeding lines also show promise of combining high yield with high protein, some of these lines may be released after one or two more years of testing. Our unit also leads the USB funded large national “Soybean Meal” research team of 18 scientists from 12 major soybean growing states. Additionally, ARS scientists have investigated mechanisms that underlie improved seed protein without a yield penalty in a high-protein line compared to its lower protein recurrent parent. In a combination of field and controlled environment experiments, scientists found that the high protein line was able to remobilize nitrogen from leaves to seeds at a higher rate during seed fill and biologically fix more nitrogen than its lower protein parent, but both phenotypes were environmentally dependent. ARS researchers are investigating the impact of management practices, such as fertilization and tillage, on seed protein. For this study, 750 plots were planted. This study includes multiple genotypes to capture genetic diversity in responses of seed protein to farm management. 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 marketplace. Populations derived from wild germplasm with higher amounts of oil and higher percentages saturated fats are in early stages of development. ARS researchers are testing more than a 1000 yield plots and 2000 progeny rows to develop high-oil lines with high yield. DROUGHT and HEAT TOLERANCE: August drought is the greatest agronomic limitation to soybean yield in the U.S. Heat stress is often overlooked in breeding programs, in part because symptoms of heat stress can be subtler than those of drought stress. ARS researchers coordinated and led over 10 scientists nationwide in a USB project on drought tolerance. To support this work, researchers grew in excess of 3000 yield plots and progeny rows of breeding lines developed from exotic drought-tolerant soybean in 2019. One of the main mechanistic hypotheses to explain the slow wilting phenotype is that some slow wilting genotypes restrict water loss when the air is very hot and dry, which results in soil moisture conservation over time. ARS researchers are also testing this hypothesis in the field with measurements of leaf-level physiology, canopy water use, atmospheric conditions, and soil moisture. In 2019, we set up the third year for this experiment, which will allow us to capture soybean responses in a wide gradient of drought conditions at Sandhills Research Station in Jackson Springs, NC. 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.

Accomplishments
1. Identification of wild soybean germplasm accessions with improved protein content and composition. Much of the value of the soybean crop comes from the meal because it is an important source of protein for humans and animals. ARS scientists in Raleigh, North Carolina, screened a diverse selection of wild soybean from the USDA soybean germplasm collections to identify those accessions with improved protein content and protein composition. Genome wide associations studies have identified genetic markers tentatively associated with these traits. Results have been published.

2. Release of low phytate soybean germplasm USDA-N6003LP. Soybean meal is the main source of protein in poultry and swine rations worldwide. Phytate, the main storage form of phosphorous in soybean seed, is indigestible by these animals resulting in phosphorus deficiency in animals and the excretion of undigested phosphorus that creates major pollution of water bodies near animal farms. Below normal field emergence of low phytate (LP) soybean is the major impediment in commercialization of LP soybean cultivars. ARS scientists in Raleigh, North Carolina, released germplasm line USDA-N6003LP with 60% lower phytate than standard cultivars and near normal field emergence. This line is an excellent parental stock for soybean breeders interested in developing LP soybean cultivars.

3. Release of high-protein soybean germplasm with competitive yield and genetic diversity USDA-N7004. Meal protein content of current U.S. soybean cultivars has dipped below the market standard (at least 48%) due to the negative correlation between seed protein and yield. To stay competitive in the international market, U.S. soybean growers and processors require high-yielding soybean with at least 48% protein in the meal. ARS scientists in Raleigh, North Carolina, recently released a germplasm line, USDA-N7004, that combines high (49%) meal protein with high yield potential. Additionally, it has 25% exotic pedigree derived from Japanese cultivar Tamahikari. This line will be very useful for both public and private soybean breeders working to develop high performing soybean cultivars with at least 48% meal protein.

4. Release of a high-yield and genetically diverse soybean germplasm, USDA-N6004. The genetic base of U.S. soybean breeding is very narrow compared to many crops, making the crop vulnerable to new threats and stymying plant breeding efforts to improve productivity. This release is part of the NP 301 effort to broaden the genetic base of soybean, reverse the trend of losing diversity, and restore vitality to soybean breeding efforts. USDA-N6004 traces 50% of its pedigree to the large-seeded Japanese cultivar Blue Side (PI 632950), and is the first U.S. release derived from this exotic accession. Blue Side is not a part of the historic genetic base of U.S. soybean. USDA-N6004 has a yield potential and maturity similar to its adapted parent, USDA cultivar NC-Roy. Thus, this release by ARS scientists at Raleigh, North Carolina, can be readily used by commercial soybean breeders to strengthen their breeding programs and develop more profitable varieties for the U.S. farmer.

U.S. DEPARTMENT OF AGRICULTURE

Soybean and Nitrogen Fixation Research: Raleigh, NC