Location: Plant Science Research
2023 Annual Report
Objectives
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.
Approach
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
Progress for this project was delayed by the loss of the lead ARS scientist. For Objective 2, six lines of Brachypodium with edits in the DMR6 gene for disease susceptibility and control wildtype plants were inoculated with wheat stem rust. Results indicate different resistance levels based on the editing event in the mutants. RNA was collected for measuring DMR6 expression in mutants and controls and converted to cDNA. Primers were designed for quantitative reverse transcription PCR assays, which are in progress. Objective 3 addresses annual coordination activities associated with the Hard Red Spring Wheat Uniform Regional Performance Nursery (HRSWURPN) program. The final step in the coordination of the 2022 nursery, involving the compilation and 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. The initial stages of coordinating this nursery program for 2023, which involved solicitation of entries from prospective participants and then orchestrating seed exchange of these entries among location cooperators, was completed. Similarly, the annual report of a second nursery program, the 2022 Uniform Regional Scab Nursery, was completed and distributed to participants, and the 2023 nursery program was coordinated in the same manner described above. The HRSWURPN has been conducted since 1929 with pdf copies of reports available for 1960 to 2002 and digitized data available from 2003 to the present at GrainGenes.org. In the past year, the paper copies of the nursery reports from 1929 to 2002 were scanned, and the majority are digitized in Excel (.xlsx), html, and comma delimited (.csv) formats with hand verification of correct and complete data sets. The availability of the historical data will be highly useful when evaluating germplasm for environmental resiliency.
Accomplishments
1. Digitization of 94 years of data from the Hard Red Spring Wheat Regional Performance Nursery. Farmers in the Midwestern United States grow hard red spring wheat varieties that are developed by breeders with ARS and land grant universities. For the past 94 years, the Hard Red Spring Wheat Uniform Regional Nursery has tested new varieties and experimental germplasm in multistate trials for yield, test weight, heading date, height, lodging, percent protein, baking qualities, and disease resistance traits. However, data from 1929 to 1960 was previously inaccessible to researchers and the public as only original hard copies existed, while reports from 1961 to 2002 were available at GrainGenes.org but data was not formatted for extraction and analysis. Starting in 2009, genetic markers for disease and agronomic traits were used on the wheat varieties grown in the nursery. ARS researchers at Saint Paul, Minnesota, had a complete set of nursery reports that they brought together into a searchable electronic format and manually curated for completeness and accuracy. These datasets contain a wealth of information to measure genetic gain over time, yield stability in different environments, and trends in disease resistance, among other traits. Historical context of the data was also included in the reports, such as grasshopper plagues, drought, leaf and stem rust epidemics. These long-term field trials led to advancements in experimental design and artificial field inoculation. The data can now be easily accessed for use in modeling to predict performance of varieties in different environments, which will be of critical use for breeders to develop locally appropriate climate-resilience varieties.
