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United States Department of Agriculture

Agricultural Research Service


Location: Plant Genetics Research

2011 Annual Report

1a. Objectives (from AD-416)
1) To develop soybeans with altered seed coat color to facilitate the segregation and identify preservation of seeds with genetically enhanced compositional traits. 2) To produce soybeans with enhanced food, feed, and industrial properties by modification of the oil and lipid-soluble antioxidant composition of seeds. 3) To introduce genes into soybeans that result in high-level accumulation of foreign and engineered proteins valuable for food, feed, and industrial uses. 4) To develop procedures and methods for analyzing and predicting seed protein allergenicity in food and feed. To develop non-allergenic seeds by supressing intrinsic allergens and to modify proteins that are potential transgenes for improving biosafety.

1b. Approach (from AD-416)
1) Co-transformation of soybean with a seed coat color-conferring transgene and a trait transgene will yield visually distinct seeds with enhanced composition. 2) Identify enzymes that are specialized for the metabolism of unusual fatty acids to produce agronomically-viable soybean seeds. 3) Manipulate protein content of soybean seeds by use of plant promotors and compartmentalization of introduced proteins. 4) Identify and characterize soybean food and feed allergens.

3. Progress Report
ARS scientists in St. Louis, MO have set up a lab that allows us to measure the elemental components (22 elements) of soybean seeds including macronutrients in fertilizer, micronutrients of significance to plant and human health, and harmful or excess elements in the soil (heavy metals, sodium, aluminum) causing agricultural or environmental problems. We have used this system to profile elite soybean cultivars that were grown in three locations around Missouri. Several elements showed significant differences in their accumulation (e.g. phosphorus) for all of the cultivars. Understanding what causes these differences will give us a better understanding of what metabolic adaptations the plants are making in response to the soil conditions. We have also used this system to begin the process of identifying genes important for elemental accumulation: 1) We profiled a mutant soybean population to look for interesting differences in elemental accumulation. From this screen we have identified over 30 potentially interesting lines, which will be grown out again and retested. Once confirmed, these lines will then be used to identify the genes causing the differences we are detecting under field grown conditions. 2) We profiled a mapping population derived from a cross between soybean and one of its wild relatives. This will allow us to identify genes that are important for improving yield with less fertilizer or on low quality soils. We developed a laboratory method of culturing seeds in a defined, controlled way to understand how they produce oil, protein and carbohydrates. To study seeds efficiently and see the impact of specific perturbations on their maturation and composition requires this controlled experimental situation. The final and successful culture conditions were derived from the result of over 100 experiments that included variation of a number of parameters and resulted in seeds that developed similar to seeds growing on the plant. We are currently altering the types of nutrients we provide the seeds and investigating the influence of each nutrient has on the seed composition. Notably there are dramatic changes in composition and in particular the amount of protein when the ratio of carbon to nitrogen provided to the seeds is changed. These investigations will lead to a better understanding of carbon partitioning within the seed and guide metabolic engineering. We have used 13-carbon isotopic labeling with this system to explore soybean seed metabolism at a subcellular level. All eukaryotes contain organelles which separate metabolic processes. The distinctions in metabolism at this compartmentalized level are not well-understood but are equally important to understanding how a seed grows at the molecular level. We have developed methods to specifically probe metabolism at this subcellular level.

4. Accomplishments
1. Genetic control of plant adaptation to unfavorable environments. Understanding how plants regulate the elemental composition (amounts of elemental nutrients such as potassium, sodium, calcium, etc.) of tissues is critical for agriculture, the environment, and human health. Each of the elements contributes to the overall nutrition of the animals that feed on soybean seeds and thus the quality and desirability of animal products for human consumption. Sustainably meeting the increasing food and biofuel demands of the planet will require growing crops with fewer inputs such as phosphorus (P) and potassium (K) and on poor soils such as those with elevated sodium (Na) levels. Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. With this technique, large quantities of data on thousands of samples can be generated. ARS scientists in St. Louis, MO used this approach to sample the natural diversity present in a model plant, the wild mustard Arabidopsis. The data was used in a genetic mapping protocol to uncover sites within the chromosomes important for elemental accumulation in the seeds of this model plant. One of these sites was important for the accumulation of Na. The scientists compared the form of the gene at this site with sites seen in each of the wild lines. Lines that contained the form of the gene that led to higher levels of Na were more likely to be from areas near the sea-coast or known high Na soils. These findings suggest that this gene provides a mechanism for plants to adapt to high Na soils. This finding has important ramifications for breeders concerned with plant nutrition as it allows them to isolate the genes that allow plants to grow and produce yield on marginal soils. The use of degrading and marginal soils for crop production is an important aspect of sustainability and the need to maintain crop yields on existing acreage, reducing the need to expand production on to new lands.

Review Publications
Thiele, I., Huduke, D.R., Steeb, B., Fankam, G., Allen, D.K., Bazzani, S., Charusanti, P., Chen, F., Fleming, R.M., Hsiung, C.A., Dekeersmaecker, S.C., Liao, Y., Marchal, K., Mo, M.L., Ozdemir, E., Raghunathan, A., Reed, J.L., Shin, S., Sigurbjornsdottir, S., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I.M., Zengler, K., Palsson, B.O., Adkins, J.N., Dirk, B. 2011. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2. BMC Systems Biology. 5:8.

Baxter, I.R., Brazelton, J., Yu, D., Huang, Y., Lahner, B., Nordborg, M., Vitek, O., Salt, D.E. 2010. A coastal cline in sodium accumulation Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genetics. 6(11). Available:

Tian, H., Baxter, I.R., Lahner, B., Salt, D.E., Ward, J.M. 2010. Arabidopsis AtNaKR1 is a phloem mobile metal-binding protein necessary for phloem function and root meristem maintenance. The Plant Cell. 22:3963-3979.

Becker, A., Chao, D., Zhang, X., Borevitz, J., Salt, D.E., Baxter, I.R. 2011. Bulk segregant analysis using single nucleotide polymorphism microarrays. PLoS One. 6(1). Available:;jsessionid=D50AD35EFC46B269B0DC1E4ECB99A37B.ambra02?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0015993&representation=PDF.

Chen, X., Alonso, A.P., Allen, D.K., Reed, J.L., Shachar-Hill, Y. 2010. Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli. Metabolic Engineering. 13:38-48.

Chao, D., Gable, K., Baxter, I.R., Chen, M., Dietrich, C.R., Cahoon, E.B., Guerinot, M., Lahner, B., Lu, S., Markham, J., Morrissey, J., Han, G., Gupta, S., Harmon, J., Jaworski, J.G., Dunn, T., Salt, D.E. 2011. Spingolipids in the root play an important role in regulating the leaf ionome in Arabidopsis thaliana. The Plant Cell. 23(3):1061-1081.

Last Modified: 06/26/2017
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