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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Research Project #424544

Research Project: Genetics and Genomics for Improving Spring Wheat with Disease Resistance

Location: Plant Science Research

2017 Annual Report

Wheat improvement is a balancing act requiring simultaneous selection for multiple diverse traits, including resistance to a range of diseases, to develop superior new cultivars. One of the diseases that is a subject of investigation here (Fusarium head blight, FHB) continues to cause significant economic losses to the U.S. wheat crop, while the other (stem rust) has the potential to do so. The overall goal of this project is to identify and characterize genes that will improve resistance to these diseases in wheat. The proposed approaches for improving wheat disease resistance will generate novel strategies, tools, and knowledge for protecting wheat against both FHB and stem rust that complement current breeding efforts for both diseases. These research activities will be coupled with the coordination of a service activity that permits wheat breeders to evaluate advanced germplasm for agronomic quality and disease resistance. Combining basic and applied research in this manner will ensure that new wheat cultivars continue to retain high yield and quality while also being protected from current and potential disease threats. To achieve project goals, three objectives will be pursued: Objective 1: Develop and evaluate hard red spring wheat with improved Fusarium head blight resistance by mapping and introgressing both a new resistance QTL and a novel genome deletion that increases resistance. Objective 2: Evaluate genotypic background effects on Fusarium head blight resistance expression by examining the genetic control of resistance suppression. Objective 3: Characterize and isolate genes for stem rust resistance from the model plant Brachypodium distachyon for introduction into wheat. Objective 4. Characterize non-host resistance to oat rust diseases in the model grass Brachypodium distachyon.

Wheat is the most widely grown crop in the world and is a major staple food 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. Both abiotic and biotic stresses can cause significant fluctuations in U.S. wheat production. Reducing current wheat losses associated with the fungal disease Fusarium head blight, and taking steps to protect the crop against the threat posed by stem rust, will increase both the stability and profitability of U.S. wheat production. This research project seeks to contribute to the goal of controlling these diseases by completing genetic, molecular genetic, and genomics research that will further our understanding of genes and molecular processes that are involved in resistance to these diseases. The results of this research will provide both new resources and new knowledge that can be used to increase resistance to Fusarium head blight and stem rust in wheat. This in turn will lead to improved wheat yields and yield stability for producers and will ensure that the U.S. wheat crop is protected against current and future disease threats.

Progress Report
During FY17, progress was made on multiple research objectives. One component of Objective 1 is focused on introducing a potential new gene for resistance to the fungal disease Fusarium head blight into wheat grown in the upper Midwest. This project was advanced one generation to create BC2F2 families that will each be segregating for the gene, in the genetic backgrounds of six adapted wheat genotypes from breeding programs at three state universities in the Midwest. A second component of Objective 1 is exploring whether Fusarium head blight resistance in wheat can be enhanced by introducing a unique deletion of part of a wheat chromosome that increases Fusarium head blight resistance. A project to introduce the deletion into wheat germplasm from breeding programs at regional universities was advanced two additional generations in the greenhouse. This has resulted in the development of BC3F2:3 near-isogenic lines of 5 adapted spring wheat genotypes that are homozygous for the deletion. A last component of Objective 1 is to provide leadership for evaluating potential new wheat varieties at multiple field locations in the upper Midwest, to assess adaptation and performance in a range of environments. The USDA-ARS has been a leader in coordinating multisite evaluations for wheat grown around the U.S for many decades. In FY17, a report on the agronomic performance of new potential wheat varieties adapted to the upper Midwest was developed for the 2016 growing season, and made publically available. Breeding programs use the information in the report to identify breeding material that may be beneficial to incorporate in their own breeding programs. This will permit continual improvement of hard red spring wheat quality and agronomic performance in the upper Midwest. Objective 2 aims to explore the presence of a putative genetic inhibitor of the Fusarium head blight resistance gene Fhb1. In the previous FY, an unexpected genetic anomaly prevented genetic mapping of this gene in the primary wheat RIL population developed for this objective. Thus, an alternative strategy was initiated. A new RIL population segregating both for Fhb1 and the postulated inhibitor gene has been evaluated with molecular markers to identify those lines that possess Fhb1. These select RILs will be evaluated for FHB resistance in future experiments, in the hope that they will be genetically stable and thus can be used to map the postulated inhibitor gene. Objective 3 involves research to understand the genetic and molecular basis of nonhost resistance to wheat stem rust in the model grass Brachypodium distachyon (Brachypodium), a relative of wheat. Using a bioinformatics approach, the genetic basis of nonhost wheat stem rust resistance was explored in a new population of F3 families from a cross between two Brachypodium genotypes. As many as 8 genome regions were identified that contribute to resistance to wheat stem rust in the most resistant families, with genes coming from both parents. In addition, genome editing using the CRISPR-Cas9 system has been initiated to identify a major gene for stem rust resistance that was previously fine mapped to an interval of fewer than 10 genes in a different Brachypodium population. The long-term objective is to use genes for nonhost wheat stem rust resistance in Brachypodium to provide an additional line of defense against this devastating wheat disease. Lastly, genome editing has also been initiated to confirm the role of a particular gene in nonhost resistance to stem rust. Previously a single base pair deletion in the gene was identified in a mutant line that has compromised resistance to stem rust, and the deletion co-segregates with susceptibility. Generation of knockouts of this gene through genome editing will provide confirmatory evidence that the deletion in the gene causes the susceptible mutant phenotype, and further implicate the gene as an essential regulator of nonhost resistance. The focus of Objective 4 is to characterize non-host resistance to oat rust diseases in Brachypodium distachyon. Research was initiated to begin to evaluate Brachypodium genotypes for genetic variation in resistance to oat stem rust and oat crown rust. Results to date indicate that such variation does exist for both diseases. The potential to explore resistance to these important oat diseases in a model system such as Brachypodium will accelerate discoveries related to enhancing resistance to these diseases in oat.


Review Publications
Gutierrez-Gonzalez, J.J., Garvin, D.F. 2017. De novo transciptome assembly in polyploid species. In: Gasparis, S., editor. Oat. Methods and Protocals. Vol 1536. New York, NY: Springer. p.209-221.
Gutierrez-Gonzalez, J., Garvin, D.F. 2016. Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of the oat genome. Plant Biotechnology Journal. 14(11):2147-2157. doi:10.1111/pbi.12571.
Des Marais, D.L., Razzaque, S., Hernandez, K.M., Garvin, D.F., Juenger, T.E. 2016. Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon. Plant Science. 251:2-11.
Woods, D., Bednark, R., Bouche, F., Gordon, S., Vogel, J., Garvin, D.F., Amasino, R. 2017. Genetic architecture of flowering time variation in Brachypodium distachyon. Plant Physiology. 173:269-279. doi:
Jiang, Y., Wang, X., Yu, X., Zhao, X., Luo, N., Pei, Z., Liu, H., Garvin, D.F. 2017. Quantitative trait loci associated with drought tolerance in Brachypodium distachyon. Frontiers in Plant Science. 8(811):1-11. doi:10.3389/fpls.2017.00811.