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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

2018 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
This research project terminated in March 2018. During the life of the project, significant advances were made in the areas of wheat genetics, in Brachypodium distachyon genome research, and in plant disease resistance. One major area of emphasis was improving resistance to the fungal disease Fusarium head blight in wheat. As part of this objective, a previously identified putative new quantitative trait locus for Fusarium head blight resistance that derives from a susceptible wheat genotype was introduced into elite hard red spring wheat germplasm from three Midwestern university wheat breeding programs. The germplasm generated is approximately 88% identical to the original elite wheat genetic backgrounds. This germplasm can be screened with molecular markers to identify plants homozygous for the new quantitative trait locus interval, and to develop new breeding lines that possess enhanced Fusarium head blight resistance. Similarly, a novel genome deletion that strongly enhances Fusarium head blight resistance was also introduced into the same elite wheat breeding lines as a second strategy to provide breeding programs with a new tool to use for improving Fusarium head blight resistance. The near-isogenic lines developed are approximately 94% identical to the original parents, and are homozygous for the deletion. Further, comparable genetic stocks that combine this deletion with the well-known partial Fusarium head blight resistance gene Fhb1 were developed. Together this germplasm provides unique resources to the breeding community to evaluate the benefit of the deletion on improved disease resistance, and to determine any negative effects of the deletion on agronomic performance. An important related activity was the annual coordination of the Hard Red Spring Wheat Uniform Regional Performance Nursery. This multi-state, multi-cooperator program was successfully completed each year during the period of this project. The data obtained and then provided back to breeding programs in the form of an annual report provided valuable data to breeders to guide selection of materials to intercross in future years, and to help make decisions about new variety releases. A related objective was to identify the chromosome location of a putative gene that inhibits the Fusarium head blight resistance gene Fhb1. Greenhouse Fusarium head blight disease evaluations of a segregating wheat population were completed, and with colleagues a genetic linkage map of this population was developed. Unexpectedly, results indicated that the region harboring the Fhb1 gene, which was initially homozygous in all individuals in the population, had been spontaneously lost in a significant proportion of the individuals. This confounded the ability to identify the chromosome location of the putative inhibitor gene. Even so, the result is significant because it implies that the resistance conferred by Fhb1 may be lost unexpectedly due to genome instability in this region of the wheat genome. Indeed, many other wheat genotypes susceptible to Fusarium head blight were found by colleagues also to lack the Fhb1 gene, which supports this contention. A third objective of this project employed the model grass Brachypodium distachyon to explore the phenomenon of nonhost resistance to the serious wheat disease stem rust. Genetic analysis of natural variation for nonhost resistance to stem rust in Brachypodium distachyon identified six genome regions with quantitative trait loci that contribute to resistance. The regions vary in size, but in some instances, contain only a few candidate genes. The cumulative amount of resistance that the quantitative trait loci contribute is large. This knowledge will guide the identification of genes involved in nonhost resistance through genome editing or other methods. A related study sought to understand the molecular basis of the loss of resistance in an induced mutant of Brachypodium distachyon. Through bioinformatic analysis, the mutation was identified and found to be a single base deletion in a gene that is a major regulator of multiple biological processes. This is the first gene identified in Brachypodium that is essential to nonhost resistance to stem rust and expands on our knowledge of the biological basis of nonhost resistance. Identifying genes for nonhost resistance to stem rust will provide a conduit for introducing a new and durable form of resistance against this disease in wheat.

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 both public and private wheat breeding programs conducted a cooperative program to evaluate the overall performance of promising new wheat germplasm at 16 locations in four states and Canada. The year 2017 was the 87th year that this program was conducted. A report detailing program results was shared with the wheat research community at large. The report provides wheat breeding programs invaluable information on the performance of their own germplasm, as well as germplasm from other breeding programs that may be incorporated into their individual breeding programs to further advance the development of new superior wheat cultivars. It also is used to make decisions about the release of superior new wheat varieties. The longevity of this cooperative program is a testament to its value to the U.S. wheat crop.