Page Banner

United States Department of Agriculture

Agricultural Research Service


Location: Genomics and Gene Discovery

2011 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.

3.Progress Report
Significant progress has been made in the genetic and molecular analysis of genes that influence economically important wheat traits.

The high molecular weigh glutenin subunit (HMW-GS) proteins are major determinants of the quality of food products made from wheat flours yet the mechanisms of how they influence dough processing properties are still poorly understood. Understanding the molecular bases of how these proteins unique to wheat function will provide new knowledge in improving the quality and nutritional properties of food derived from wheat. To this end, scientists at WRRC utilized an in vitro reconstitution system to study the contributions of variant allele protein products and specific domains of HMW-GS proteins in dough properties. Equal amount of Dx and Dy-type subunits was found to result in greatest synergistic effects and that the length of the repetitive domain in these proteins is important for dough processing.

Low temperature is a major abiotic stress that limits the growth, productivity and geographical distribution of agricultural crops. Even in established agricultural production areas, seasonal or episodic freezing events can lead to significant crop loss. The identification and characterization of genetic factors that are critical for low temperature tolerance are needed for the development and improvement of germplasms with a wide spectrum of tolerance to extreme temperatures. Expression of genes in cold-hardy and cold-sensitive cultivars of wheat was compared using DNA microarrays. Results identified genes that may play critical roles in the development of tolerance to low temperature. Fundamental insights into the regulation of these cold responsive genes were gained.

Data derived from the next generation sequencing (NGS) of total genomic DNA from diploid wheat Aegilops tauschii (D-genome contributor) were annotated and used to develop a genome-wide single nucleotide polymorphism (SNP) discovery pipeline. A total of 195,631 putative SNPs dispersed across the entire A. tauschii genome were discovered.

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. The sequence of the genome of Brachypodium distachyon was completed through collaborative efforts. A high-density genetic linkage map was generated and used to compare the Brachypodium genome features to other grasses.

1. Brachypodium genome sequenced. Model systems play an important role in studies of genome structure and evolution and are invaluable in the isolation of agronomically important genes/traits for functional characterization. Brachypodium has numerous attributes expected in a genetic model and interest in using it as model system for wheat and other temperate grasses is growing rapidly. Models are particularly important for wheat and barley because they are difficult experimental systems. The sequencing of the Brachypodium genome will impel the development of Brachypodium as an experimental model system for grasses. The comparison of the Brachypodium gene sequences has shown the close relationship to wheat and is being used to confirm wheat gene sequences. Brachypodium has a small genome, fast life cycle, easy transformation and closer genetically to wheat and barley than any other plant model.

2. Genes critical for the development of cold tolerance in wheat identified. The impending global climate change does not only predict an increase in absolute ambient temperature but also an increase in global climate variability, which could lead to more warm winters or cold spells during spring or summer. Agricultural production is highly dependent on weather and environmental conditions. Damage due to freezing of crops is the major source of economic loss compared to any other weather hazards. Comparison of the expression of genes in cold-hardy and cold-sensitive wheat cultivars led to the identification of genes that could play critical roles in the development of low temperature tolerance. Identifying and understanding the mechanisms required for growth in low temperature is crucial to the development of cold-tolerant crops.

Review Publications
Akhunov, E.D., Akhunova, A., Anderson, O.D., Anderson, J., Blake, N., Clegg, M., Coleman-Derr, D., Conley, E., Crossman, C., Deal, K., Dubcovsky, J., Gill, B., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Luo, M., Ma, Y., Matthews, D.E., Mcguire, P., Morrell, P., Qualset, C., Renfro, J., Tabanao, D., Talbert, L., Tian, C., Toleno, D., Warburton, M., You, F., Zhang, W., Dvorak, J. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. Biomed Central (BMC) Genomics. 11:702-710.

Massa, A.N., Wanjugi, H., Deal, K.R., Chan, A.P., Gu, Y.Q., Luo, M., Anderson, O.D., Rabinomics, P.D., Dvorak, J., Devos, K.M., O'Brien, K., Maiti, R., You, F. 2011. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Molecular Biology and Evolution. Available at: http://mbe.oxfordjournalsorg/content/early/2011/04/06/molbev.msr080.long. DOI: 10.1093/molbev/msr080.

Stamova, B., Chingcuanco, D.L., Beckles, D. 2010. Transcriptomic analysis of starch biosynthesis in the developing grain of hexaploid wheat. International Journal of Plant Genomics. Available at: http://www.hindawi com/journals/ijpg/2009/407426/. doi:10.1155/2009/407426.

Chingcuanco, D.L., Ganeshan, S., You, F., Fowler, B., Chibbar, R., Mcguire, P., Anderson, O.D. 2011. Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature. Biomed Central (BMC) Genomics. 1:299.

Last Modified: 7/25/2014
Footer Content Back to Top of Page