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ARS Home » Midwest Area » St. Paul, Minnesota » Plant Science Research » Research » Research Project #434207

Research Project: Novel Strategies for Durable Disease Resistance in Wheat and Oat

Location: Plant Science Research

2020 Annual Report

Crop 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) continues to cause significant economic losses to the U.S. wheat crop, while another (stem rust) has the potential to do so. Similarly, crown rust continues to be a significant disease of oat. The overall goal of this project is to use genetic engineering technologies to develop novel molecular variants of specific genes and validate that they, as well as a previously identified spontaneous mutation, improve resistance to these particular diseases in wheat and oat. The approaches for improving disease resistance will generate novel resources and knowledge for protecting wheat against both FHB and stem rust, and oat against crown rust, in a manner that complements current breeding efforts for both diseases. These research activities will be coupled with the coordination of a service activity that provides a conduit for Midwestern hard red spring wheat breeders to evaluate jointly their advanced germplasm for agronomic quality and disease resistance at multiple locations. Combining basic and applied research in this manner will ensure that new wheat and oat cultivars 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: Evaluate a novel wheat genome deletion that improves Fusarium head blight resistance in adapted hard red spring wheat under field conditions. Sub-Objective 1.A. Evaluate the effect of genetic background on Fusarium head blight resistance conferred by a novel genome deletion. Sub-Objective 1.B. Evaluate the effect of pyramiding the deletion and the partial FHB resistance gene Fhb1 on suppression of FHB. Sub-Objective 1.C. Evaluate the effect of the deletion on agronomic performance in contemporary hard red spring wheat. Objective 2: Establish efficient transformation systems in parallel for wheat and oats, and improve disease resistance by endogenous gene disruption and foreign gene addition. Sub-Objective 2.A. Validate candidate rust susceptibility genes in the model grass Brachypodium. Sub-Objective 2.B. Disrupt stem rust susceptibility genes in wheat. Sub-Objective 2.C. Disrupt crown rust susceptibility genes in oat. Objective 3: Coordinate the Hard Red Spring Wheat Uniform Regional Performance Nursery Program.

Objective 1 seeks to enhance Fusarium head blight resistance in hard red spring wheat by introducing a unique genome deletion that improves resistance to this disease. We will determine if the deletion will improve resistance in other susceptible wheat genotypes. Near-isogenic lines of two susceptible hard red spring wheat cultivars that either possess or do not possess the deletion have been developed. These lines will be evaluated in Fusarium head blight nurseries at several locations to determine if lines with the deletion exhibit improved Fusarium head blight resistance when compared to the lines that do not possess it. We will test whether the deletion, when paired with a Fusarium head blight resistance gene, enhances Fusarium head blight resistance synergistically. Near-isogenic lines of two Fusarium head blight-susceptible hard red spring wheat cultivars that possess either the resistance gene alone or the gene together with the deletion will be evaluated in Fusarium head blight nurseries to determine if lines with both the deletion and the resistance gene exhibit superior resistance compared to the lines with resistance agene alone. We will examine how the deletion affects agronomic performance. The deletion has been introduced into diverse hard red spring wheat breeding lines. These near-isogenic lines and the original parents will be grown in field plots at several locations. Agronomic traits will be measured in the near-isogenic lines and compared to their parents to determine if the deletion has a detrimental effect on them. Objective 2 seeks to improve resistance to wheat stem rust and oat crown rust. We will employ the model grass Brachypodium as a testbed to test if mutating certain genes enhances resistance to these diseases. Genome editing using the CRISPR/Cas9 system will be used to perturb the genes, which are known or thought to enhance resistance to pathogens in other plant species when disrupted, in Brachypodium. Plants with confirmed mutations in the genes will be inoculated with the pathogens that cause wheat stem rust and oat crown rust, to confirm that their disruption improves resistance to these diseases. We will build on these results by creating, in wheat, mutations in the genes that enhance stem rust resistance in Brachypodium, and determining whether they also improve stem rust resistance in wheat. We will also create mutations in these same genes but in oats, to determine whether enhanced crown rust resistance can be obtained. Objective 3 will provide hard red spring wheat breeding programs in the upper Midwest an annual opportunity to have their advanced wheat germplasm evaluated for performance at more than a dozen field sites in fives states and Canada. The advanced lines are planted in replicated plots at these locations, and agronomic trait data on the germplasm are obtained by colleagues at each location.

Progress Report
In FY2020, progress was made on several research projects that comprise the project plan. First, grain of wheat near-isogenic lines that contain a chromosomal deletion that improves resistance to the fungal disease Fusarium head blight was again distributed to spring wheat breeding colleagues at three Midwestern universities. This germplasm has been planted by them in field disease trials in three locations across these states and will be evaluated for resistance for a second time in 2020 for Fusarium head blight resistance, both to determine whether the deletion improves resistance in susceptible wheat genotypes under field conditions, and to determine whether the deletion interacts in a positive manner with the Fusarium head blight resistance gene Fhb1 to improve resistance. A related project seeks to determine how the aforementioned deletion impacts agronomic properties of wheat. The deletion has been introduced into several elite wheat genotypes from spring wheat breeding programs at three Midwestern universities. A field plot seed increase of this material is being completed in two separate locations, and the grain that is obtained will be planted in the Spring of 2021 at three locations to obtain agronomic trait data to determine if the deletion has any deleterious effects. A related project was with an ARS colleague at Fargo, North Dakota sought to determine if milling and baking properties are altered due to the deletion. The results suggest that the deletion does not negatively impact a spectrum of traits such as bread loaf volume. A different area of research being pursued as part of the project plan involves the use of gene editing to improve disease resistance in wheat and oats, by disrupting so-called disease susceptibility genes. Proof of concept studies with the model grass Brachypodium distachyon have advanced, with each of the three target genes selected for the project having successfully been disrupted by a well-established gene editing method. The gene editing events have so far been confirmed to be inherited in the offspring of the initial transgenic plants for two of the three genes. Initial transgenic plants targeting a fourth potential susceptibility gene have also been produced. In parallel, research to develop an efficient transformation method for oats was undertaken. This will be needed to translate findings from the Brachypodium research above to this crop species. Two different methods for transforming oat were evaluated. One involves the transformation of oat embryos, and the other involves the transformation of callus tissue. Evidence of transformation using both methods was obtained, and the overall frequency of transformation was quite high, based on transient expression of a marker gene. The ability to induce callus production from oat embryos has now been greatly improved by a technical alteration to the method being employed. Lastly, the final stage of the coordination of the 2019 Hard Red Spring Wheat Uniform Regional Performance Nursery, involving the analysis of agronomic performance data of elite wheat germplasm at multiple locations in four states and development and dissemination of a final report, was completed. Similarly, the first stages of coordinating the 2020 Hard Red Spring Wheat Uniform Regional Performance Nursery, including soliciting germplasm entries, developing the final list of germplasm entries for this year’s evaluations, and then organizing seed distribution to the program’s location cooperators, were completed.

1. Development of a new genomics resource for oat improvement. Oats have higher concentrations of health-promoting compounds such as beta-glucan than other cereal crops, but new genomics tools lag behind these other crops. ARS researchers in Saint Paul, Minnesota, in collaboration with colleagues at Cornell University, developed a new, robust transcriptome assembly for oat seeds. This research tool was then used to identify the relationship between expression differences in certain genes among different oat lines and variation for various health promoting compounds in oat seeds. These results provide new opportunities to selectively alter the levels of health-promoting properties of oats through manipulation of genes that are associated with them.

Review Publications
Hu, H., Gutierrez-Gonzalez, J.L., Liu, X., Yeats, T.H., Garvin, D.F., Hoekenga, O.A., Sorrels, M.E., Gore, M.A., Jannink, J. 2020. A new oat seed transcriptome identifies heritable temporal gene expression patterns in developing seeds of hexaploid oat. Plant Biotechnology Journal. 18(5):1211-1222.