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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetics Research

2013 Annual Report

1a. Objectives (from AD-416):
1. The long-term goal of this Objective is to develop soybean seeds that have increased oil levels derived at the expense of non-structural carbohydrates. 2. Molecular biology techniques will be used to improve the nutritional quality of soybean seed proteins. 3. To develop the molecular basis for modification of the fatty acid components of soybean oil and anti-nutritional components in soybean meal to use in accelerated breeding programs. 4. Identify effects on key performance determinants of crop seed quality resulting from modified seed composition using traditional or non-traditional genetic methods.

1b. Approach (from AD-416):
To reach the overridging objective of the modification of soybean seed composition for food, feed, and industrial uses requires a team approach that spans the complete range from basic biochemical assessment of possible target sites to the evaluation of the agronomic properties and value of modified soybeans. Basic biochemical approaches will be used to assess the effect of manipulating the expression of a key enzyme complex that is at the interface of carbon partitioning into oil or carbohydrates. A proteomic approach to the analysis of soybean seed development will allow for the discovery of other key regulatory events that offer possibilities for manipulation. Transgenic approaches will be used to modify the protein content and constitution of the soybean seed such that the nutritional quality as feed can be improved. A similar approach combined with classical molecular genetic approaches to plant breeding will be directed at altering the fatty acid components and anti-nutritional compounds of soybean seed to improve not only the nutritive value of the seed but also the health aspects of soybean consumption. A classical physiological approach serves to address the efficacy of the targeted modifications as they relate to agronomic concerns of yield, seed quality, and storage.

3. Progress Report:
A first-stage systems biology platform for analysis of soybean seed development has been prepared. The platform is based primarily upon results from analysis of carbon-centric metabolism. This particular direction was initially targeted because two of the end-point targets for modification are the triacylglycerol storage oil and the raffinosaccharide antinutrients. However, protein quality is a secondary target so it was important to include results from some analysis of nitrogen and sulfur metabolism. We have addressed the former using the regulatory enzyme glutamine synthase as a probe. Results supported a model where nitrogen metabolism/protein accumulation takes place at an earlier time point than carbon metabolism/oil accumulation. This information will lead us to shift emphasis on modifying oil accumulation to a later point in seed development. Understanding sulfur metabolism in soybeans requires multi-component analysis. Soybean seeds are deficient in the sulfur-containing amino acids when used as feed for monogastric animals such as pigs and fowl. A key enzyme for sulfur assimilation was overexpressed in developing seeds. This provides an improved source for sulfur. The gene encoding a sulfur-rich seed storage protein from maize was expressed in developing soybeans. This provides an improved sink for sulfur. By increasing both the source and sink of sulfur, soybeans were developed that have a statistically significant increase in both amino acid and protein-sulfur. If the results can be validated, the projected increase in the sulfur-amino acid cysteine should be adequate to satisfy the nutritional requirements of monogastric animals. Allele haplotypes were determined in the publically available 31 re-sequenced soybean genomes. In addition, allele haplotypes were determined for the 41 re-sequenced soybean genomes provided to us from the nested association mapping (NAM) project parent lines. We analyzed a selected set of genes involved in basic phenotypic traits such as flower color, pubescence color, and photoperiod response as well as seed composition related genes involved in fatty acid synthesis, tocopherol modification, and seed carbohydrate partitioning. New software has been developed and is being refined for use in analysis of single nucleotide polymorphisms in genes of interest from whole genome re-sequence data.

4. Accomplishments

Review Publications
Hagely, K., Palmquist, D.E., Bilyeu, K.D. 2013. Classification of distinct seed carbohydrate profiles in soybean. Journal of Agricultural and Food Chemistry. 61:1105-1111. Available:

Gillman, J.D., Baxter, I.R., Bilyeu, K.D. 2013. Phosphorus partitioning of soybean lines containing different mutant alleles of two soybean seed-specific adenosine triphosphate-binding cassette phytic acid transporter paralogs. The Plant Genome. 6:1-10.

Natarajan, S.S., Krishnan, H.B., Khan, F.H., Chen, X., Garrett, W.M., Lakshman, D.K. 2013. Analysis of soybean embryonic axis proteins by two-dimensional gel electrophoresis and mass spectrometry. Journal of Basic and Applied Sciences. 9:309-332.

Flores-Ramirez, G., Janecek, S., Miernyk, J.A., Skultety, L. 2012. In silico biosynthesis of virenose, a methylated deoxy-sugar unique to Coxiella burnetii lipopolysaccharide. Proteome Science. 10:67.

Ahsan, N., Huang, Y., Tovar-Mendez, A., Swatek, K.N., Zhang, J., Miernyk, J.A., Xu, D., Thelen, J. 2013. A versatile mass spectrometry-based method to both identify kinase client-relationships and characterize signaling network topology. Journal of Proteomics. 12(2):937-948.

Miernyk, J.A., Johnston, M.L. 2013. Proteomic analysis of the testa from developing soybean seeds. Journal of Proteomics. 89:265-272.

Krishnan, H.B., Chen, M. 2013. Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase. Journal of Agricultural and Food Chemistry. 61:5404-5409.

Last Modified: 10/18/2017
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