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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

2022 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
Objective 1: We conducted multi-location field tests with soybean germplasm containing the appropriate maturity gene alleles as well as the targeted seed composition allele combinations. The germplasm represented maturities between Maturity Group 0 and 5, and seeds were produced in North Dakota, two locations in Minnesota, Illinois, four Missouri environments, and Tennessee. Yield tests were performed in two Missouri environments. The composition analyses for fatty acids in the seed oil and seed carbohydrate profiles revealed stable expression of the targeted traits, without obvious interference. We expanded our original goals by developing and testing additional experimental germplasm that included a new allele for reduced raffinose synthase enzyme activity that was discovered and characterized in collaboration with an ARS researcher in West Lafayette, Indiana. In general, soybean germplasm with semi-determinate stem architecture alleles did not perform well in the standard yield trials, but that germplasm may perform better in specialized trials. Two genetic mapping populations were developed for high seed protein content from ‘Mead’ and ‘Bonus’ that can be phenotyped and genotyped in fiscal year 2023. There has been considerable interest in accessing ARS soybean germplasm with seed composition traits for evaluation as grain and/or as a source of alleles for those traits. We continued working with collaborators to develop and refine applied genomics tools. We discussed soybean as the premier source of plant-based protein with other scientists and stakeholders. Objective 2: Research continued towards determining the genetic architecture responsible for soybean seed value and abiotic stress tolerance. We grew out a heat-tolerance mapping population at four locations but suffered two separate disasters: a flood destroyed one field location and a greenhouse malfunction destroyed a heat-stress experiment. With only two locations for which we could collect data we were unable to identify any significant quantitative trait loci. As such, we were unable to meet the 48-month milestone. Nevertheless, we made substantial progress towards completing Sub-objective 2.4 and the 60-month milestone: final crosses to generate our novel multi parent advanced generation intercross population were completed and validated and the final population is being advanced now. Objective 3: Research continued toward improving the overall sulfur amino acid content of soybeans. Two enzymes in sulfur assimilatory pathway, O-acetylserine sulfhydrylase (OASS) or Adenosine triphosphate sulfurylase (ATPS), play crucial roles in sulfate assimilation and regulate the overall sulfur amino acid content of seed. Previously, we have reported the development of transgenic soybean plants that independently overexpress in these two enzymes. By employing traditional breeding approach, we have now obtained homozygous transgenic soybean plants that simultaneously overexpress OASS and ATPS. These soybean plants were subjected to in- depth biochemical and molecular characterization. Both proteomic and RNA sequencing analysis were conducted leading to the identification of several key candidate genes and proteins that could play a key role in regulating the overall concentration of sulfur amino acids in soybean seeds. Our results indicate that simultaneously overexpressing both OASS and ATPS is a viable approach to enhance the sulfur amino acid content of soybean seeds.

1. Developed applied genomics tools for soybean and other crop species to accelerate discovery of genetic improvements in agriculture. The generation of whole genome sequence information for crops has accelerated past the point of full analysis capacity for any single research program; therefore, the full value of the genomic information is lost. Whole genome sequence information contains the sequence variants in and around genes that define the characteristics plant breeders select for and against to improve crops, but next generation analysis tools are needed to identify those variants. ARS researchers in Columbia, Missouri, and collaborators are pioneering the pairing of bioinformatics and molecular biology to develop new accessible tools and strategies to leverage whole genome sequence information for crop improvement. The research team developed a vision for a species-independent applied genomics framework and conducted research in the area of applied genomics. The research led to gene-based analyses of the soybean genome and the development of a suite of online tools hosted by the collaborator. The tools all work for soybean genomic data, and the Allele Catalog Tool has been generalized for other species with initial efforts also leading to Maize Allele Catalog and Arabidopsis Allele Catalog tools. Six applied genomics tools are now available online. The applied genomics research area is evolving rapidly, and the new tools and strategies are available but not yet widely used. The research results provide the soybean research community as well as other agricultural biologists with tools and technologies to accelerate their own discovery research for genetic improvement of agriculturally important species.

Review Publications
Kaler, A.S., Purcell, L., Beissinger, T., Gillman, J.D. 2022. Genomic prediction models for traits differing in heritability for soybean, rice, and maize. Biomed Central (BMC) Plant Biology. 22. Article 87.
Krishnan, H.B., Kim, S., Pereira, A.E., Jurkevich, A., Hibbard, B.E. 2022. Adenanthera pavonina, a potential plant-based protein resource: seed protein composition and immunohistochemical localization of trypsin inhibitors. Food Chemistry: X. 13. Article 100253.
Dietz, N., Chan, Y., Scaboo, A., Graef, G., Hyten, D., Happ, M., Diers, B., Lorenz, A., Wang, D., Joshi, T., Bilyeu, K.D. 2022. Candidate genes modulating reproductive timing in elite US soybean lines identified in soybean alleles of Arabidopsis flowering orthologs with divergent latitude distribution. Frontiers in Plant Science. 13. Article 889066.
Song, B., Qiu, Z., Li, M., Luo, T., Wu, Q., Krishnan, H.B., Wu, J., Xu, P., Zhang, S., Liu, S. 2022. Breeding of ‘DND358’: a new soybean cultivar for processing soy protein isolate with a hypocholesterolemic effect similar to that of fenofibrate. Journal of Functional Foods. 90. Article 104979.
Krishnan, H.B., Jurkevich, A. 2022. Confocal fluorescence microscopy investigation for the existence of subdomains within protein storage vacuoles in soybean cotyledons. International Journal of Molecular Sciences. 23(7). Article 3664.
Chamarthi, S.K., Kaler, A.S., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Dhanapal, A.P., King, C.A., Purcell, L.C. 2021. Identification and confirmation of loci associated with canopy wilting in soybean using genome wide association mapping. Frontiers in Plant Science. 12. Article 698116.
Dietz, N., Combs-Giroir, R., Cooper, G., Stacey, M., Miranda, C., Bilyeu, K.D. 2021. Geographic distribution of the E1 family of genes and their effects on reproductive timing in soybean. Biomed Central (BMC) Plant Biology. 21. Article 441.
Islam, N., Krishnan, H.B., Natarajan, S.S. 2021. Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development. Proteomics. Article e2100143.
Kim, J., Scaboo, A., Pantalone, V., Li, Z., Bilyeu, K.D. 2022. Utilization of plant architecture genes in soybean to positively impact adaptation to high yield environments. Frontiers in Plant Science. 13. Article 891587.
Nieto-Veloza, A., Zhong, Q., Kim, W., D'Souzaa, D., Krishnan, H.B., Dia, V.P. 2021. Utilization of tofu processing wastewater as a source of the bioactive peptide lunasin. Food Chemistry. 362. Article 130220.
Islam, N., Krishnan, H.B., Natarajan, S.S. 2022. Protein profiling of fast neutron soybean mutant seeds reveal differential accumulation of seed and iron storage proteins. Phytochemistry. 200. Article 113214.
Basnet, P., Meinhardt, C.G., Usovsky, M., Gillman, J.D., Joshi, T., Song, Q., Diers, B., Mitchum, M.G., Scaboo, A. 2022. Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations. Theoretical and Applied Genetics. 135:2025-2039.
Sarkar, S., Shekoofa, A., Mcclure, A., Gillman, J.D. 2022. Phenotyping and quantitative trait locus analysis for the limited transpiration trait in an upper-mid south soybean recombinant inbred line population (“Jackson” × “KS4895”): high throughput aquaporin inhibitor screening. Frontiers in Plant Science. 12. Article 779834.