Location: Genomics and Gene Discovery
2010 Annual Report
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.
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.