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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND MOLECULAR APPROACHES TO WHEAT TRAITS
2010 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) Use combinations of molecular alterations, heterologous expression, and plant transformations in the application of molecular biology and genetic engineering to wheat high-molecular-weight (HMW) glutenin class seed storage protein genes and other seed protein classes to understand more of the molecular bases of wheat quality and utilization. .
2)Contribute to the understanding of the organization of the wheat genome through in-depth studies of wheat seed protein genetic loci and participation in national and international wheat genome characterization projects. .
3)Employ DNA microarrays to profile gene expression during wheat seed development and changes in storage protein gene activity and wheat quality..
4)Contribute to the development of Brachypodium as a model for small grains research, to include use in studying wheat seed protein gene controls. Previously was 5325-21430-011-00D (10/03). Replacing 5325-21000-011-00D (04/08).


3.Progress Report
We have made significant progress in the genetic and molecular analysis of genes that influence economically important wheat traits.

Among the dietary essential amino acids, the most severely limiting in the cereals is lysine. The breakdown of lysine is controlled mainly by the catabolic bifunctional enzyme lysine ketoglutarate reductase - saccharopine dehydrogenase (LKR/SDH). The analysis of a wheat LKR/SDH gene and comparative structural and functional analyses among available plant genes provides new information on this important gene. Both the structure of the LKR/SDH gene and the immediately adjacent genes show lineage-specific differences between monocots and dicots, and findings suggest variation in activity of LKR/SDH genes among plants. Evidence for monofunctional SDH transcripts shows a novel intron in wheat, Brachypodium, and poplar.

Expression of genes involved in starch synthesis in wheat was analyzed with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses using DNA microarrays. The results showed multiple temporal expression patterns of key genes involved in starch synthesis.

Wheat HMW-glutenin protein subunit genes are often the primary targets for biotechnological improvement of the breadmaking quality of wheat fours because of their primary role in determining food processing properties. Understanding the evolution of these wheat unique proteins could help elucidate the molecular bases of expression and function of these seed storage proteins. Comparative sequence analyses of genomic regions corresponding to the wheat HMW-glutenin genes from eight different grass species/genomes revealed that the wheat HMW-glutenin genes resulted from an ancient duplication of a globulin gene, implying the importance of sequence duplication in storage protein gene evolution.

We previously developed unique repeat DNA junction marker (RJMs) for mapping in polyploid wheat. A software tool, RJPrimers, was further developed for high accurate identification of unique repeat junctions and automated primer design for mapping. Analysis of shotgun genomic sequences generated by Roche 454 sequencing technology indicated that one RJM marker per 10 kb in wheat genome.

The on-going project to develop and utilize Brachypodium as a model system for Triticeae research for grain quality and other traits has progressed significantly. We completed the construction of Brachypodium genome physical map and performed genome-wide comparison with wheat and rice. The Brachypodium physical map represents an important resource for grass comparative genomics and useful for comparative mapping in wheat.


4.Accomplishments
1. Genes for seed starch synthesis identified. Seed starch is the major storage compound in cereals providing as much as 80% of the calories consumed by mankind. Starch is also a major source of feed, fiber, biofuel, and biopolymers in many industrial applications. ARS scientists in Albany, CA used wheat DNA microarrays to study the expression of genes involved in starch synthesis. The results were overlaid with the analysis of soluble sugar accumulation, starch content, and starch granule particle size distribution. The results showed multiple temporal expression patterns of key genes involved in starch synthesis and identified many candidate genes for further characterization of their roles in seed starch synthesis and potential targets for modulating carbohydrate metabolism in wheat by genetic engineering or molecular breeding efforts.

2. Large DNA library constructed in model grass. Model systems play an important role in studies of genome structure and evolution and are invaluable in isolation of agronomically important genes/traits for functional characterization. Brachypodium has numerous attributes expected to find in a genetic model and interest in using it as model system for wheat and other temperate grasses is growing rapidly. To foster the development of Brachypodium as a grass model, several critical genomics resources need to be available for public access. A high resolution BAC-based physical map has many genomics applications including analyzing genome structure, conducting genome-wide comparison, facilitating the genome assembly, and final completion of the genome sequencing by filling gaps. ARS scientists in Albany, CA, developed a high resolution BAC-based physical map of the Brachypodium genome in collaboration with UC Davis. This resource has facilitated Brachypodium genome assembly and comparative analysis with rice and wheat. A project website was developed for public access to request genomic resources developed by this project.


Review Publications
Anderson, O.D., Coleman-Derr, D., Gu, Y.Q., Heath, S. 2010. Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme. Biomed Central (BMC) Genomics. 10:113.

Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F., Lazo, G.R., Nelson, W., Soderlund, C., Dvorak, J. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. Biomed Central (BMC) Genomics. 10:496

Fleury, D., Luo, M., Dvorak, J., Ramsay, L., Gill, B., Anderson, O.D., You, F., Schoaei, Z., Deal, K., Langridge, P. 2010. Physical mapping of a large plant genome using global high-information content fingerprinting: a distal region of wheat chromosome 3DS. Genetics. 11:382.

You, F., Wanjugi, H., Huo, N., Lazo, G.R., Luo, M., Anderson, O.D., Dvorak, J., Gu, Y.Q. 2010. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Research. 38:Suppl:W310-320.

Gu, Y.Q., Wanjugi, H., Coleman-Derr, D., Kong, X., Anderson, O.D. 2009. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins. Functional and Integrative Genomics. 10:111-122.

Last Modified: 12/20/2014
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