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United States Department of Agriculture

Agricultural Research Service

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Location: Plant Science Research

2009 Annual Report

1a. Objectives (from AD-416)
The overall goal of this research plan is to identify and characterize genes that can be used to improve disease resistance in wheat. Four objectives will address this goal. Objective 1: Use marker-assisted selection to introduce new Fusarium head blight (FHB) resistance into hard red spring wheat. Objective 2: Use transcript profiling and virus-induced gene silencing (VIGS) to identify wheat genes involved in resistance to rust pathogens. VIGS will be completed in collaboration with Steve Scofield, ARS West Lafayette, Indiana. Objective 3: Use the model plant Brachypodium distachyon (Brachypodium) to identify and validate genes involved in stem rust resistance in wheat. Objective 4: Coordinate the Uniform Regional Performance Nursery for Spring Wheat Parents. Wheat improvement is a balancing act because it requires the simultaneous selection of multiple diverse traits to develop superior new cultivars. Two of the three diseases that are subjects of investigation here (FHB, leaf rust) presently cause economic losses to the U.S. wheat crop, while the third disease (stem rust) has the potential to do so. By taking a multidisciplinary approach to improving wheat disease resistance as proposed in this research plan, multiple avenues for protecting wheat against these three diseases will become available. Providing strategies, knowledge, and tools for improving wheat disease resistance, as delineated by the first three objectives, will lead to reduced yield losses attributable to FHB and leaf rust, and will ensure that the potential disease threat from stem rust can be addressed proactively. The fourth objective subsequently provides an opportunity for all spring wheat breeders to evaluate the overall performance of advanced germplasm, including assessment of resistance to FHB, leaf rust, and stem rust, in addition to overall agronomic quality.

1b. Approach (from AD-416)
Wheat is the most widely grown crop in the world and is a major staple crop for humans. Wheat is economically very important to the United States, which ranks third among all countries in wheat production and is the world's largest wheat exporter. Despite its importance as a crop, low prices that are generally paid for wheat grain result in small profit margins for producers. Further, both abiotic and biotic stresses can cause significant fluctuations in U.S. wheat production. Reducing wheat losses associated with the fungal diseases Fusarium head blight, leaf rust, and stem rust will enhance both the stability and profitability of U.S. wheat production. This research project seeks to contribute to the goal of controlling these three diseases by completing integrated genetic, molecular genetic, and genomics research that will further our understanding of genes and underlying molecular processes in wheat that are involved in resistance to each of these diseases. The results of this research will provide both new resources and new knowledge that can be used to increase resistance to each of these three diseases in wheat. This will lead to improved wheat yield and yield stability and will ensure that the U.S. wheat crop is protected against current and future disease threats.

3. Progress Report
During FY 2009 the genome sequence was analyzed of the model grass Brachypodium distachyon. This was an international effort that provides what is considered to be the most complete and accurate plant genome sequence completed to date. The first molecular map of Brachypodium was completed in FY 2009. It can be used for a variety of purposes by plant researchers. The molecular marker data came from several laboratories participating in a collaborative effort. New genetic stocks of Brachypodium were developed, namely the first recombinant inbred lines for this species. A crossing protocol for Brachypodium was developed and an illustrated document was produced and made available to interested colleagues (see Stem rust resistance was evaluated in several dozen Brachypodium lines, and a pilot genetic analysis of stem rust resistance in Brachypodium was completed. We evaluated different doses of gamma irradiation to introduce novel mutations in Brachypodium, and these have been screened to identify putative mutants with altered stem rust resistance. We also furthered Fusarium head blight (FHB) resistance research projects. A set of approximately 100 F2-derived F3 wheat lines segregating for a putative new FHB resistance QTL was evaluated in the greenhouse in winter/spring 2009. Additional FHB resistance research included comparative analyses of the effect of this new QTL and Fhb1, a resistance gene that to date confers the greatest level of protection against the disease. Our results suggest that the new QTL we are seeking to map can have an effect at least equal to Fhb1. Molecular markers that may tag this new putative FHB resistance QTL have been identified, and DNA from the aforementioned segregating population has been isolated for use in molecular mapping research to confirm the identity of markers that are associated with improved FHB resistance. We advanced the introgression of Fhb1 into triticale, a feed grain with little FHB resistance. We have completed three backcrosses, and this material will now be selfed and lines homozygous for Fhb1 will be selected for greenhouse and field evaluation of FHB resistance. As part of coordinating the Hard Red Spring Wheat Uniform Regional Performance Nursery (URN), a report detailing results of the 2008 nursery was written and distributed (see and the coordination of the 2009 URN was initiated. Similar efforts were completed for a second nursery coordinated – the Uniform Regional Scab Nursery for Spring Wheat Parents (see

4. Accomplishments
1. Genome Sequence Analysis for New Model Grass Grasses form the basis of human nutrition and are promising sources of renewable energy. The cool season wild grass Brachypodium distachyon holds great promise as a model system for structural and functional analysis of genes important to grass crop improvement. A scientist in the Plant Science Research Unit in St. Paul, MN, co-directed a DOE-supported international project to completely decipher the compact genome sequence of Brachypodium and analyze its gene content and genome organization relative to economically important grass crops. Brachypodium has approximately 25,000 genes, including approximately 180 that possess hallmarks of disease resistance genes. The genome sequence of Brachypodium was readily aligned to genomes of rice and sorghum and to genetic maps of wheat and barley. The complete Brachypodium genome sequence and associated comparative data obtained will pave the way for the next generation of biological discovery in grass crops.

Review Publications
Garvin, D.F., Stack, R.W., Hansen, J.M. 2009. Quantitative Trait Locus Mapping of Increased Fusarium Head Blight Susceptibility Associated with a Wild Emmer Wheat Chromosome. Phytopathology. 99(4):447-452.

Bolton, M.D., Kolmer, J.A., Xu, W., Garvin, D.F. 2008. Lr34-Mediated Leaf Rust Resistance in Wheat: Transcript Profiling Reveals a High Energetic Demand Supported by Transient Recruitment of Multiple Metabolic Pathways. Molecular Plant-Microbe Interactions. 21(12):1515-1527.

Bolton, M.D., Kolmer, J.A., Garvin, D.F. 2008. Wheat Leaf Rust Caused by Puccinia triticina. Molecular Plant Pathology. 9(5):563-575.

Kolmer, J.A., Singh, R.P., Garvin, D.F., Viccars, L., William, H.M., Huerta-Espino, J., Ogbonnaya, F.C., Raman, H., Orford, S., Bariana, H.S., Lagudah, E.S. 2008. Analysis of the Lr34/Yr18 Rust Resistance Region in Wheat Germplasm. Crop Science. 48(5):1841-1852.

Last Modified: 2/23/2016
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