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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Research Project #434147

Research Project: Gene Discovery and Designing Soybeans for Food, Feed, and Industrial Applications

Location: Plant Genetics Research

2020 Annual Report

Objective 1: Identify new soybean alleles, or effective combinations of existing genes, that positively impact commercially relevant oil or meal traits; work with breeders to incorporate them into modern backgrounds; confirm their expression or effectiveness under field conditions; and determine value in food or feed applications. Objective 2: Identify and verify new genomic regions in soybean associated with improved stress tolerance, seed constituent (oil and protein), and quality traits, and use genomic strategies such as genetic mapping and genome analysis to make new genes rapidly available to breeders. Objective 3: Develop novel strategies to increase concentrations of S-containing amino acids and to reduce levels of trypsin inhibitor and allergens; work with breeders to develop soybean germplasm that combine these genes in high protein backgrounds to meet the animal nutrient requirements.

Obj 1- New soybean germplasm will be developed with combinations of the high oleic-low linolenic oil trait and low raffinose oligosaccharide meal trait that is targeted to different maturity groups (MG). Seeds produced in an appropriate environment will be evaluated for trait interactions, environmental stability, protein and oil content, and yield. We will establish a novel panel of approximately 400 soybean accessions from the National Plant Germplasm System (NPGS) and conduct genome-wide association studies (GWAS) with protein and oil data. Mutant soybean lines will be screened to identify seed composition variants. Obj 2- We will use a four pronged approach in order to dissect the genetic architecture underlying soybean seed value (principally seed oil and protein content) and abiotic stress adaptation: 2.1) a new GWAS using a diverse panel of 380 MG III genotypes to maximize genetic diversity within a very narrow maturity range; 2.2) Genomic Prediction to estimate seed composition breeding values for all 2,011 MG III accessions; 2.3) Fine mapping of a heat-tolerance trait from an exotic landrace; and 2.4) Development of a Multi-Parent Advanced Generation Inter-Cross (MAGIC) population. We will evaluate the potential of Genomic Prediction to predict seed composition and select parents with maximal genetic potential for developing a MAGIC population. We will Fine-map a previously identified major effect QTL associated with tolerance to heat-induced-seed-degradation. Obj 3- We will develop and characterize soybean germplasm with increased sulfur (S)-containing amino acids and decreased anti-nutritional factors. To enhance the S amino acid content, we plan to overexpress an enzyme in the sulfur assimilation pathway. Additionally, high-protein soybean experimental lines lacking Kunitz trypsin inhibitor (KTI) and ß-conglycinin, will be developed using a traditional breeding approach. In order to verify if overexpression of tow enzymes simultaneously will further increase the overall S-amino acid content, we will characterize ATPS and OASS activity in greenhouse grown material from genetic crosses between overexpressing transgenic soybeans lines. To better understand the chilling stress responses in soybean, a comparative proteomic analysis will be performed.

Progress Report
Activities throughout the year directed at Objective 1 were to select for the targeted alleles of seed composition and maturity genes in experimental soybean germplasm and confirm the effect of the targeted allele combinations in the appropriate environments. This effort was successful for the combination of oil and meal traits targeted to maturity groups 0 as well as II through IV and IV semi-determinate. The high oleic acid and low linolenic acid oil traits produced the expected fatty acid profiles, and the altered carbohydrate phenotype was consistent from prior analyses in our maturity group III/IV environment as well as seed produced in a maturity group II environment. For the oil plus meal trait combination, the remaining desired experimental germplasm was processed through an additional year of population development for final allele selection in the current field season. The association panel analysis revealed a potential source for elevated seed protein content that will be further explored with the goal of maintaining oil levels and increasing yield. Significant progress towards completion of Objectives 2.1-2.4 has been made. We completed a Genome Wide Association Study (12 month milestone) and identified a number of important genomic regions controlling seed compositional traits, which also permitted creation of a genomic prediction model to identify the most divergent lines from the ARS germplasm collection for seed composition. A three-location field study was completed in 2020 and all seed data has been collected. These results validated our genomic prediction model and met our 24-month milestone. In addition, we completed our 36-month milestone a year ahead of schedule; initial crossing was successfully completed in 2019, and additional intercrossing is planned for the summers of 2020 and 2021. When complete, these efforts will yield a unique Multiparent Advanced Generation InterCross population combining the best possible genetic potential for seed composition (seed protein/oil, improved oil and carbohydrate profiles) with seed yield alleles and two distinct forms of abiotic stress tolerance (drought and elevated temperature). We have also made progress towards our 48-month milestone and identified near-isogenic lines for a major effect Quantitative Trait Locus (QTL) conferring tolerance to elevated temperatures. Initial greenhouse-based experiments will commence this summer. Substantial progress towards Objective 3 has been made. Adenosine triphosphate (ATP) sulfurylase, an enzyme which catalyzes the activation of sulfate to adenosine 5'-phosphosulfate (APS), plays a significant role in controlling sulfur metabolism in plants. We have generated transgenic soybean plants that constitutively overexpress ATP sulfurylase. Compared with that of untransformed plants, the ATP sulfurylase activity was about 2.5-fold higher in developing seeds. Soybean seeds overexpressing ATP sulfurylase accumulated very low levels of the ß-subunit of ß-conglycinin. The accumulation of the cysteine-rich proteins was several folds higher in transgenic soybean plants when compared to the non-transgenic wild type seeds. Sulfate, cysteine, and some sulfur-containing secondary metabolites accumulated in higher amounts in ATP sulfurylase transgenic seeds. Additionally, over expression of ATP sulfurylase resulted in 37-52% and 15-19% increases in the protein-bound cysteine and methionine content of transgenic seeds, respectively. Our results demonstrate that manipulating the expression levels of key sulfur assimilatory enzymes could be exploited to improve the nutritive value of soybean seeds.

1. A new type of soybean for healthier soybean oil. Soybean oil was the world’s premier source of vegetable oil but lost the market in human foods due to changes in regulations that affected the most widely used processed version of the oil containing trans fats. With the lost market came negative pressure on soybean prices as the value of the oil was discounted, and alternative vegetable oils produced outside the United States were sourced. Molecular biology research by ARS researchers at Columbia, Missouri, along with collaborators, led to the discovery of two changes in the soybean genome that resulted in a seed oil with zero trans fats and full functionality for use in food applications like cooking and frying. ARS researchers at Columbia, Missouri, led a team of seven public university plant breeders to translate these two genetic changes for high oleic acid along with two previously discovered genome changes for low linoleic acid to create novel soybean germplasm and high yielding soybean varieties across all U.S. maturity groups with the high oleic/low linolenic acid oil trait. This high oleic trait was patented, and stakeholders are participating in the licensing and marketing efforts for the new soybean type. One commercial sales license has been executed to date. This research delivered a solution to a food health issue that also positively affects the price farmers receive for a key commodity. The industry goal is to grow 16 million acres of high oleic acid soybeans by 2026.

Review Publications
Kaler, A.S., Gillman, J.D., Beissinger, T., Purcell, L.C. 2020. Comparing different statistical models and multiple testing corrections for association mapping in soybean and maize. Frontiers in Plant Science. 10:1794.
Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2020. Nested association mapping of important agronomic traits in three interspecific soybean populations. Theoretical and Applied Genetics. 133:1039-1054.
Miranda, C.A., Scaboo, A., Cober, E., Denwar, N., Bilyeu, K.D. 2020. The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments. Biomed Central (BMC) Plant Biology. 20:65.
Darr, L., Cunicelli, M., Bhandari, H., Bilyeu, K.D., Chen, F., Hewezi, T., Li, Z., Sams, C., Pantalone, V. 2020. Field performance of high oleic soybeans with mutant FAD2-1A and FAD2-1B genes in Tennessee. Journal of the American Oil Chemists' Society. 97:49-56.
Wei, X., Kim, W., Song, B., Oehrle, N.W., Liu, S., Krishnan, H.B. 2020. Soybean mutants lacking abundant seed storage proteins are impaired in mobilization of storage reserves and germination. ACS Omega. 5(14):8065-8075.
Do, P.T., Nguyen, C.X., Bui, H.T., Tran, L.T., Stacey, G., Gillman, J.D., Zhang, Z.J., Stacey, M.G. 2019. Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2-1A and GmFAD2-1B genes to yield a high oleic, low linoleic and a-linolenic acid phenotype in soybean. Biomed Central (BMC) Plant Biology. 19:311.
Gillman, J.D., Biever, J.J., Ye, S., Spollen, W.G., Givan, S.A., Lyu, Z., Joshi, T., Smith, J.R., Fritschi, F.B. 2019. A seed germination transcriptomic study contrasting two soybean genotypes that differ in terms of their tolerance to the deleterious impacts of elevated temperatures during seed fill. BMC Research Notes. 12:522.
Miranda, C.A., Xu, Q., Oehrle, N.W., Islam, N., Garrett, W.M., Natarajan, S.S., Gillman, J.D., Krishnan, H.B. 2019. Proteomic comparison of three extraction methods reveals the abundance of protease inhibitors in the seeds of grass pea, a unique orphan legume. Journal of Agricultural and Food Chemistry. 67(37):10296-10305.
Kaler, A., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Purcell, L.C. 2020. Genome-wide association mapping of dark green color index using a diverse panel of soybean accessions. Scientific Reports. 10.
Hagely, K., Jo, H., Kim, J., Hudson, K.A., Bilyeu, K. 2020. Molecular-assisted breeding for improved carbohydrate profiles in soybean seed. Theoretical and Applied Genetics. 133:1189-1200.