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United States Department of Agriculture

Agricultural Research Service

Research Project: Modification of Soybeans for Food, Feed, and Industrial Applications

Location: Plant Genetics Research

2013 Annual Report


1a.Objectives (from AD-416):
The team objective is design and development of soybean seeds with modified-composition that can be used in both new agronomic applications and improved/modified/specialized versions of traditional applications. The multidisciplinary experimental plan incorporates strategies from genomics, systems biology, biochemistry, physiology, genetics, and breeding. Progress from each of the single objectives will be constantly monitored to see if changes in experimental strategies are warranted. Objective 1: Verify and integrate proteomic changes, differentially expressed proteins, metabolic footprints, and ionomic profiles of soybean seed development, and combine with genomics to develop novel strategies for seed improvement. Objective 2: Develop novel strategies to produce increased S-containing amino acids and decreased anti-nutritional factors in soybean seeds, determine interactions among traits, and create soybean germplasm with increasing levels of these amino acids and reducing levels of anti-nutritional factors. Objective 3: Determine source and combinations of alleles in the soybean germplasm collection that can be used to contribute positive influence on soybean oil and meal components to improve concentration and quality. Objective 4: Determine the role of environmental stress on soybean seed growth and quality traits, and develop novel strategies to produce seeds containing increased oil and protein concentration with enhanced quality.


1b.Approach (from AD-416):
Develop an interactive, knowledge-based quantitative systems description of soybean seed development using computational analyses of data from targeted-proteomic analyses, transcript profiling, metabolomic profiling, and ionomic studies.

To utilize the systems model to determining the step(s) that are limiting oil production and accumulation, and provide a basis for increasing oil levels without decreasing proteins levels, as well as decreasing levels of anti-nutritional compounds and increasing protein quality. The model will also provide insight into the system response to perturbation. This will help with the design of potential changes that will likely require a coordinated multi-level approach.

To improve the nutritional quality of soybean seed meal. A two-pronged approach, including metabolic engineering of S assimilatory pathway genes plus expression of genes encoding S-rich proteins will be used to design soybean with elevated S amino acid content. Additionally, elimination of Kunitz trypsin inhibitor (KTI), an anti-nutritional component of soybean meal, will be accomplished using a RNA interference (RNAi) approach.

To develop soybean germplasm with improved oil and meal quality traits a combination of reverse-genetics, forward genetics, genomics, and breeding, will be employed. The main focus is on development of reverse genetic resources for improving oil and meal quality by discovery of candidates for modification of oil quality including alleles, from both induced and natural sources, encoding proteins involved in FA biosynthesis, TAG biosynthesis, and TAG packaging/storage in oil bodies.

To develop and characterize value-added soybean germplasm with improved seed quality and enhanced germination efficiency will be approached by screening plant introduction lines with tolerance to supra-optimal temperatures during seed development and used to determine the underlying genetic bases. Similarly, lines with enhanced germination at sub-optimal soil temperatures will be identified by screening of germplasm resources. Sexual crosses to high yielding commercial cultivars and seed compositional alterations will be performed and analysis of the resulting populations will be used to map and evaluate the ability of these traits to compensate for abiotic stress-sensitivity.


3.Progress Report:
1. Both chemical and biological methods to analyze seed protein modifications have been optimized for study of soybeans. Combinations of chemical and computational methods have been used to determine the precise position of modification within the protein sequence. This information will be important in understanding results from studies of how proteins interact with other proteins.

2. The elemental sulfur content of several soybean lines was determined. Lines selected as high sulfur are being grown in different environments. Mineral analysis of these seeds will enable us to document environmental effects on seed sulfur content.

3. To accelerate our breeding efforts for the increased bio-available vitamin E trait, a molecular marker assay for the published variant allele controlling the phenotype was developed. The molecular marker assay was used to identify individual soybean plants containing the alleles from a segregating population. After the selected plants are mature, they will be evaluated for the seed phenotype.

4. The genotyping by sequencing (GBS) methods developed for study of maize have been optimized for use in studies of soybean, and applied to an F5 population segregating for tolerance/sensitivity to heat-induced seed degradation. Our GBS pipeline yielded 6000 polymorphic markers between the tolerant and sensitive parental lines, and an average of 4822 marker genotypes for each line in the population. Analysis of quantitative trait loci will begin as soon as phenotypic data are available.


Last Modified: 12/22/2014
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