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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

2016 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 FY16, 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. We used simple sequence repeat molecular markers that are in proximity to the resistance gene to begin the process of introducing the resistance gene into adapted wheat germplasm from wheat breeding programs at three state universities in the Midwest by marker-assisted backcrossing. 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. Greenhouse increases of wheat germplasm that combine the deletion and the Fusarium head blight resistance gene were completed, and five near-isogenic lines of two different susceptible wheat cultivars were identified that exhibited morphological similarity to the cultivars. These near-isolines are scheduled to be used for disease evaluations in order to determine if the deletion combined with the resistance gene increases resistance. Simultaneously, we advanced a project to use marker-assisted backcrossing to introduce the deletion into wheat germplasm from wheat breeding programs at regional universities two additional generations. This prebreeding is being completed to proactively develop new breeding germplasm for these programs should the deletion improve resistance. Objective 2 is exploring a putative genetic inhibitor of a major Fusarium head blight resistance gene using data from wheat single nucleotide polymorphism arrays obtained from a mapping population that is segregating for this hypothetical inhibitor gene and for which disease data was previously obtained, collaborative research with an Australian scientist revealed the potential genome location of this inhibitor. However, an unexpected finding emerged from the population analysis; a significant number of the lines that constitute the mapping population had spontaneously deleted the Fusarium head blight resistance gene, and so the action of the putative inhibitor gene could not be assessed in those lines. This confounds further analysis and so alternative strategies for confirming the location of the inhibitor gene are being considered. 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 new bioinformatic approaches involving high throughput sequencing and bulked segregant analysis, the genetic basis of nonhost wheat stem rust resistance was assessed in a population segregating for resistance to wheat stem rust. Seven regions of the Brachypodium genome were identified that contribute to resistance to wheat stem rust. In addition, a potential causal mutation in the Brachypodium genome that causes wheat stem rust susceptibility was identified using a different bioinformatic approach. The mutation, a 1 base pair deletion, modifies the sequence of a gene by introducing a premature stop codon. Support for this mutation being the cause of wheat stem rust susceptibility in the mutant is found in previous Arabidopsis research where a homologous gene, when perturbed, results in increased disease susceptibility. The long-term objective for both studies is to use genes for nonhost wheat stem rust resistance in Brachypodium to provide an additional line of defense against this potentially devastating wheat disease. The focus of Objective 4 is to provide support 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 FY16, a report on the agronomic performance of new potential wheat varieties adapted to the upper Midwest was developed for the 2015 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.

1. Unraveling the genetic control of nonhost resistance to wheat stem rust. Global wheat production is threatened by new forms of wheat stem rust that defeat many existing stem rust resistance genes. One promising strategy for protecting wheat from stem rust involves a poorly understood type of resistance called nonhost resistance. Using the model grass Brachypodium distachyon, a wild relative of wheat that is a nonhost for wheat stem rust, the genetic control of nonhost resistance was determined to involve genes located at seven chromosome locations. This finding provides the first step toward isolating nonhost resistance genes in Brachypodium for use in constructing a new and durable layer of resistance to stem rust in wheat, and in turn increasing food security by protecting global wheat production.

Review Publications
Garvin, D.F., Porter, H., Blankenheim, Z., Chao, S., Dill-Macky, R. 2015. A spontaneous segmental deletion from chromosome arm 3DL enhances Fusarium head blight resistance in wheat. Genome. 58(11):479-488.
Cass, C.L., Lavell, A.A., Santoro, N., Foster, C.E., Karlen, S.D., Smith, R., Ralph, J., Garvin, D.F., Sedbrook, J.C. 2016. Cell wall composition and biomass recalcitrance differences within a set of Brachypodium distachyon inbred lines. Frontiers in Plant Science. 7:708.
Garvin, D.F. 2015. Brachypodium distachyon genetic resources. In: Vogel J.P. editor. Genetics and Genomics of Brachypodium. Springer International: Gewerbestrasse, Switzerland. p. 183-195.