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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND MOLECULAR APPROACHES TO WHEAT TRAITS

Location: Genomics and Gene Discovery

2012 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.

Mapping and map-based cloning of agriculturally and economically important traits for crop wheat improvement remain a great challenge due to its large and complex genome. For the same reason, complete sequencing of wheat genome still represents a daunting task. Generation of valuable genomics resources could greatly facilitate various aspects of wheat research. In collaborative efforts, various high resolution maps including genetic, physical, and radiation hybrid maps have been generated. These maps are widely accessible to the wheat research community. The development of bacterial artificial chromosome-based physical map for the wheat D genome provides a foundation for future sequencing of the entire wheat D genome.

The high molecular weight 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 wheat. To this end, scientists at WRRC screened wheat mutant lines that are deficient in genes encoding the HMW-GS to understand the changes of chemical and physical properties associated with the lack of expression of individual HMW-GS in mutant lines. This is the first time that the role of individual HMW-GS has been examined in vivo. In addition, the Unit published an extensive study of the roles of different regions of the HMW-GS play in dough quality and identified factors in dough characteristics.

The substantial increases of wheat yield were made possible by introducing dwarfing traits into modern wheat cultivars. Therefore, the dwarf trait in crops has contributed greatly to the sustainable food supply demanded by the increasing world population. A large genomic region spanning a severe dwarfing gene region has been sequenced. Comparative analysis with rice, Brachypodium, and sorghum indicated a high sequence conservation among grass species. New cis-regulatory elements that control/regulate the expression of the dwarfing gene were identified, facilitating future biotechnological application of these regulatory elements for crop improvement.

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. Over 10,000 T-DNA insertional mutant lines have been generated for functional genomics study in this model species. Brachypodium genes involved in lignin biosynthesis has been functionally characterized to understand the cell wall structure and function. In addition, a viral resistance gene has been identified and mapped in Brachypodium. This is the first demonstration that Brachypodium can be exploited for isolation of resistance genes for important crops.


4.Accomplishments
1. Developed an integrated genetic and physical map for the wheat D genome. The international wheat sequence consortium adopted a clone-by-clone sequencing strategy to produce a gold standard reference sequence for the wheat genome. A prerequisite for such sequencing method is the development of physical maps consisting of overlapping clones. ARS scientists in Albany, California, collaborated with University of California Davis, on developing a high resolution BAC-based physical map of Ae. tauschii, the D genome donor of bread wheat. The 4,020 Mb Ae. tauschii genome is the largest and most complex genome for which a physical map has been assembled. The use of this map for ordering gene sequences and advancing knowledge of grass genome evolution has been demonstrated. A project website has been developed for public access to search molecular markers and BAC contigs for gene mapping and cloning as well as genome-wide comparative study.

2. Useful wheat genetic stocks developed. Prolamins are the major seed storage proteins in wheat flour. Among them, High Molecular Weight (HMW) glutenin proteins determine the end-use products in food processing. To generate genetic diversity of genes controlling HMW-glutenin contents and compositions, ARS scientists in Albany, California, generated wheat lines deficient in HMW-glutenin genes using chemical mutagenesis method. The production of HMW-glutenin deficient lines makes it possible to determine the effects of individual HMW-glutenin genes on the properties of the wheat dough. The availability of these useful genetic stocks will facilitate the development of different varieties of wheat with defined dough functionality for specific end-use.


Review Publications
Duan, J., Wu, J., Gu, Y.Q., Kong, X. 2012. New cis-regulatory elements in the Rht-D1b locus region of wheat. Functional and Integrative Genomics. Available at: http://rd.springer.com/article/10.2007/s10142-012-0283-2. DOI 10.1007/s10142-012-0283-2.

Chingcuanco, D.L. 2012. Isolation and characterization of EMS-induced Dy10 and Ax1 high molecular weight glutenin subunit deficient mutant lines of elite hexaploid wheat (Triticum aestivum L.) cv. Summit. Journal of Cereal Science. 56:296-299 doi: 10.1016/j.jcs.2012.06.009.

Kumar, A., Bassi, F.M., Gu, Y.Q., Dogramaci, M., Kianian, S. 2012. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. Biomed Central (BMC) Genomics. doi 10.1186/1471-2164-13-339.

Wu, J., Gu, Y.Q., Hu, Y., You, F.M., Dandekar, A.M., Leslie, C.A., Aradhya, M.K., Dvorak, J., Luo, M. 2011. Characterizing the walnut genome through analyses of BAC end sequences. Plant Molecular Biology. 78:95-107.

Chingcuanco, D.L., Fowler, B.D. 2012. Genotype dependent burst of transposable element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation. Comparative and Functional Genomics. Available at: http://www.hindawi.com/journals/cfg/2012/232530/. doi:10.1155/2012/232530..

Li, Y., Xioa, J., Wu, J., Gu, Y.Q., Kong, X. 2012. A tandem segmental duplication (TSD) in the green revolution gene Rht-D1b region underlies plant height variation. New Phytologist. doi: 10.1111/j.1469-8137.2012.04243.x.

Anderson, O.D., Bekes, F., D'Ovidio, R. 2011. Effects of specific domains of high-molecular-weight glutenin subunits’ on dough properties by an in vitro assay. Journal of Cereal Science. 54:280-287.

Anderson, O.D., Bekes, F. 2011. Incorporation of high-molecular-weight glutenin subunits into doughs using 2 gram mixograph and extensigraphs. Journal of Cereal Science. 54:288.

Last Modified: 8/30/2014
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