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United States Department of Agriculture

Agricultural Research Service


Location: Genomics and Gene Discovery

2008 Annual Report

1a.Objectives (from AD-416)
1) Apply molecular biology and genomics to understand the structure, function and expression of wheat seed protein genes;.
2)Contribute to the understanding of the organization of the wheat genome, with a focus on the group 1 chromosomes; and.
3)Develop and utilize Brachypodium as a model system for Triticeae research for grain quality and other traits.

1b.Approach (from AD-416)
1) Apply molecular biology and genetic engineering to wheat high-molecular-weight (HMW) glutenin class seed storage protein genes and other protein classes to understand the molecular bases of their contributions to wheat quality and utilization. Methods will include combinations of molecular alterations, heterologous expression, and plant transformations. .
2)Determine the structure and variability of wheat quality-related genetic loci and contribute to the understanding of the organization of the wheat genome. .
3)The complement of genes active in wheat seed development will be further developed through expressed-sequence-tags (ESTs). .
4)Develop gene expression profiles across wheat seed development and changes in storage protein gene activity and wheat quality. Employ DNA microarrays to profile gene expression during wheat seed development, investigate profile changes during changes in storage protein composition, and will identify candidate genes related to seed traits.

3.Progress Report
Wheat is an important staple crop and serves as the greatest single source of protein in the human diet – accounting for approximately 20% of the total protein consumed by humans worldwide. However, cloning and manipulating genes controlling important traits for crop improvement remains a great challenge in wheat due to the complexity of its large genome. Understanding the genome complicity and development of genomics tools for wheat improvement is the focus of the project. Molecular markers useful for genotyping and marker-assisted breeding have been generated. We completed developing 240 single nucleotide polymorphism markers (SNP) for group 1 chromosomes in the hexaploid wheat. Brachypodium distachyon has become an emerging model system for temperate grasses, including wheat and barley, due to its small genome size and other desirable traits. The knowledge gained from Brachypodium can directly apply to research on important crops. This year we completed the sequence of the entire chloroplast genome of Brachypodium and conducted the detailed comparison of chloroplast genomes from different related grass species. Detailed comparative map covering the short arm of wheat group 1 chromosomes was generated based on comparison with the colinear region from Brachypodium.

The HMW-glutenin subunit protein is a major determinant of wheat grain end-use quality, thus, is an obvious target for protein modification to improve wheat flour functionality. It has been hypothesized that since the HMW-glutenin subunits are synthesized primarily as storage proteins with no other known biological function, changing its composition or level will not substantially affect the other grain components. To begin to test this hypothesis we evaluated the changes in the metabolic network of wheat grain due to the over-expression of the gene encoding the high-molecular-weight (HMW) glutenin Dx5-subunit. We compared the metabolite profiles of developing caryopses of two independent transformants over-expressing Dx5 and two independent transformants expressing only the selectable-marker gene (controls). Analysis of our data was unable to reveal any distinction between the Dx5 transformants and the controls suggesting that their metabolite compositions were similar. Our results indicate that the over-expression of the gene encoding the HMW-glutenin subunit does not substantially alter the metabolic composition of the grain.

This relates to National Program 301, Component 2.

1. Sequencing the chloroplast genome of Brachypodium. Plastids are key organelles of green plants, carrying out many important functions such as photosynthesis and starch storage. In addition to their important biological roles, plastids have the potential to make great biotechnological impact through plastid transformation. The completed sequence of the Brachypodium chloroplast, done by ARS scientists in the Genomics and Gene Discovery Research Unit in Albany, CA, genome provides genome information to study evolution of the chloroplast genome as well as to understand the biogenesis of chloroplast organelle. This project aligns with National Program 301 - Plant Genetic Resource, Genomics, and Genetic Improvement, Component II – Crop Informatics, Genomics, and Genetic Analysis, Problem Statement A – Structural Comparison and Analysis of Crop Genome.

2. Metabolic profiling of transgenic wheat over-expressing HMW-glutenin. Plant biotechnology offers a great potential for genetic engineering of important traits for crop improvement. Expression of HMW-glutenin genes in wheat leads to enhanced biochemical and biophysical features related to wheat baking quality. To understand if over-expression of HMW-glutenin resulted in any metabolic changes, ARS scientists in the Genomics and Gene Discovery Research Unit in Albany, CA used a global metabolic profiling approach to assess metabolic network changes in the transgenic wheat. Our result verified that HMW-glutenin primarily serves as a storage protein during seed development. This work supports the possible manipulation of the composition and amount of other storage proteins in the grain to improve its quality. This accomplishment of this project aligns with National Program 301 - Plant Genetic Resource, Genomics, and Genetic Improvement, Component II - Genomic Characterization and Genetic Improvement, Problem Statement C- Genetic Analysis and Mapping of Important Traits.

6.Technology Transfer


Review Publications
Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., Gu, Y.Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes. 1:61.

Last Modified: 4/20/2014
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