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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

2015 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 FY15, progress was made on a number of research objectives. First, as part of an effort to introduce a potential new gene for resistance to the fungal disease Fusarium head blight into wheat to grown in the upper Midwest (Objective 1), we identified three simple sequence repeat molecular markers that are in proximity to the resistance gene based on linkage analysis. These are now being used to introduce the resistance gene into adapted wheat germplasm from regional university wheat breeding programs in Minnesota, North Dakota, and South Dakota by marker-assisted backcrossing. In a related project, we are seeking to enhance Fusarium head blight resistance using a novel strategy: introducing into disease-susceptible wheat a unique deletion of part of a wheat chromosome that increases Fusarium head blight resistance (Objective 1). We successfully completed genetically combining this deletion with the best known and most widely used gene for Fusarium head blight resistance in two separate disease susceptible wheat backgrounds, using marker-assisted breeding. These new genetic stocks will be used to evaluate the benefit of having both the gene and the deletion present to further reduce disease damage. Simultaneously, we are introducing the deletion into adapted hard red spring wheat germplasm from regional university wheat breeding programs in Minnesota, North Dakota, and South Dakota to proactively generate breeding materials for these programs. We advanced the development of this material one generation by marker-assisted backcross selection. A third project (Objective 2) is seeking to understand why, in one particular wheat variety, the aforementioned Fusarium head blight resistance gene rarely increases resistance. In just one of several genetic stocks we developed from this variety to contain Fusarium head blight resistance gene do we observe increased disease resistance. Thus, we are examining the genetic basis of this phenomenon in a wheat population segregating for what we believe is a genetic inhibitor of Fusarium head blight resistance gene. We completed replicated experimental greenhouse disease evaluations of this population in fall 2014 and spring 2015, which revealed evidence of one or more segregating inhibitory genes. We also obtained genotypic data for use in identifying molecular markers for the hypothesized inhibitor genes, by genotyping the population using wheat single nucleotide polymorphism arrays. The long-term goal is to use this information to improve resistance to this major disease. A last area of research (Objective 3) we are exploring is the molecular control of resistance to the disease wheat stem rust, on plant species which it cannot infect. Termed nonhost resistance, this type of resistance is very robust and affords long-term protection to the disease. We are employing the model grass Brachypodium distachyon (Brachypodium), a relative of wheat that is a nonhost to wheat stem rust, to identify genes that control the process of nonhost resistance. We evaluated the genetic control of wheat stem rust multiple times in a population developed between parents with contrasting levels of resistance. It appears that two or more genes are involved in susceptibility to wheat stem rust, in contrast to what we observed for another form of stem rust that infects the forage grass timothy. In addition, a separate population developed between a resistant genotype and a mutant that exhibits compromised resistance was evaluated in disease screens. The mutant phenotype segregated as a single locus, and DNA pools from sets of resistant and susceptible individuals were created and are being sequenced using high throughput sequencing. The sequence information obtained will be employed for bioinformatic analysis to localize the mutation in the Brachypodium genome. Our long-term objective for both projects is to use genes critical to nonhost stem rust in Brachypodium to reconstruct critical components of its nonhost resistance response in wheat. This will provide an additional line of defense against this potentially devastating wheat disease. Lastly, a key aspect of continual improvement of U.S. wheat varieties is rooted in evaluating performance of potential new varieties at multiple locations, to assess adaptation and performance in a range of environments (Objective 4). The USDA-ARS has been a leader in coordinating multisite evaluations for wheat grown around the U.S for many decades. In FY15, a report on the agronomic performance of new potential wheat varieties adapted to the upper Midwest was developed for the 2014 growing season, and made publically available. Breeding programs can use information in the report to identify breeding materials in other programs that would be beneficial to include in their own breeding programs. This will permit continued improvement of hard red spring wheat quality and agronomic performance in the upper Midwest.

1. Ensuring the competitiveness of U.S. wheat. Hard red spring wheat grown in the Upper Midwest is considered the premium wheat grown in the U.S. To ensure that this wheat market class retains this designation, ARS scientists in St. Paul, Minnesota, in conjunction with public and private wheat breeding programs conducted a cooperative program to evaluate the overall performance of promising new wheat germplasm at 13 locations in four states. 2014 was the 84th year that this program was conducted. A report detailing program results was shared with the wheat community at large, and provides breeding programs invaluable information on their own germplasm as well as germplasm from other programs that may be desirable to incorporate into their breeding programs. The longevity of this program is a testament to its value to the U.S. wheat crop.

Review Publications
Catalan, P., Chalhoub, B., Chochois, V., Garvin, D.F., Hasterok, R., Manzaneda, A.J., Mur, L.A., Pecchioni, N., Rasmussen, S., Vogel, J.P., Voxeur, A. 2014. Update on the genomics and basic biology of Brachypodium: International Brachypodium Initiative (IBI). Trends in Plant Science. 19:414-418.
Faris, J.D., Zhang, Z., Garvin, D.F., Xu, S.S. 2014. Molecular and comparative mapping of genes governing spike compactness inherited from wild emmer wheat. Molecular Genetics and Genomics. 289:641-651.
Gordon, S.P., Priest, H., Des Marais, D., Schackwitz, W., Figueroa, M., Martin, J., Bragg, J., Tyler, L., Lee, C., Bryant, D., Wang, W., Messing, J., Manzaneda, A., Barry, K., Garvin, D.F., Budak, H., Tuna, M., Mitchell-Olds, T., Pfender, W.F., Juenger, T., Mockler, T., Vogel, J.P. 2014. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant Journal. 79:361-374.
Zhong, S., Ali, S., Leng, Y., Wang, R., Garvin, D.F. 2015. Brachypodium distachyon-Cochliobolus sativus pathosystem is a new model for studying plant-fungal interactions in cereal crops. Phytopathology. 105:482-489.