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United States Department of Agriculture

Agricultural Research Service

Research Project: Soybean Seed Improvement Through Quantitative Analysis of Phenotypic Diversity in Response to Environmental Fluctuations

Location: Plant Genetics Research

Project Number: 3622-21000-039-00
Project Type: Appropriated

Start Date: Jul 23, 2013
End Date: Jul 22, 2018

Objective:
Objective 1: Determine interactions of elemental profiles with environment at the molecular level, and use this knowledge to develop strategies to predict responses of soybeans to abiotic stresses, and discover useful genes for improving soybean seed quality traits. Sub-objective 1.1: Large scale ionomic profiling to identify genetic loci and gene by environment interactions controlling elemental accumulation and identify elemental signatures of plant physiological responses to the environment. Sub-objective 1.2: Comparative genetics and RNAi experiments to identify and test genes in soybean. Objective 2: Use flux analysis to improve understanding of carbon, energy and redox partitioning in soybean tissues, and develop computational methods that provide spatial or temporal descriptions of metabolism in the seed. Sub-objective 2.1: Use isotopic labeling approaches to describe the flow of carbon in developing embryos from glutamine taken up to pyruvate-derived storage reserves. Sub-objective 2.2: Describe the operation of pentose phosphate pathway (PPP) metabolism in developing soybeans.

Approach:
Goal 1.1.A: Identify genes controlling elemental accumulation in many different environments. Goal 1.1.B: Identify elemental signatures of plant responses to stressful environments. The ionome is a highly sensitive probe of the processes that allow plants to adapt to the soil environment. The mechanisms that plants use to adapt to different soil environments will affect how they take up elements and different mechanisms will have different effects on the ionome. By identifying the genes responsible for elemental accumulation, we will also be identifying the genes responsible for adapting to the environment. Additionally, it may be possible to identify elemental signatures of different mechanisms of adaptation to the environment. Goal 1.2.: Identify and test candidate genes in soybeans and the oilseed model Camelina. The results from Approach 1 will give us a large number of genomic regions that control ionomic traits. For most of these regions, we will not be able to identify the causative loci directly in soybean. Instead, we will need to employ a variety of computational methods to identify candidate genes. The most powerful methods are likely to be comparative genomics efforts leveraging the large amount of ionomic data from other organisms to identify candidates that can then be addressed directly in soybean. Goal 2.1.A: Determine the contribution of glutamine carbon to the production of pyruvate-derived amino and fatty acids through the use of malic enzyme. Goal 2.1 B: Determine the carbon sources for citrate biosynthesis in seeds and its subsequent use for oil and or protein amino acid production. We will pursue a more explicit understanding of the role for carboxylic acids and related enzymes by i) developing methods for transient isotopic labeling of embryos with organic acids or amino acids and ii) analyzing labeled products with LC-MS/MS and scintillation counting to assess the redistribution of the label over time, quantifying metabolic fluxes when applicable. Goal 2.2: Demonstrate that oxidative and non-oxidative pathways within PPP maintain the production of erythrose-4-phosphate and ribulose-5-phosphate, necessary for amino acid and nucleotide production under different reduced/oxidized status. We will investigate the operational status of pentose phosphate pathway (PPP) metabolism in developing soybeans. The organization of PPP in soybeans is structured to produce aromatic amino acid precursors and nucleotides under changing redox conditions while fixing carbon or additionally producing NADPH depending upon development and the environment. The current investigations will also utilize isotopic labeling investigations and potentially flux analysis with paralleled technique developments.

Last Modified: 7/31/2014
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