Location: Plant Science Research
2019 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
In FY2019, progress was made on several projects. First, seed of wheat near-isogenic lines that contain a unique chromosomal deletion that improves resistance the fungal disease Fusarium head blight was increased and distributed to colleagues at three universities. This germplasm has been planted by them in field plots in three Midwestern states and will be evaluated in the summer of 2019 for Fusarium head blight resistance both to determine whether the deletion improves resistance in diverse susceptible wheat genotypes under field conditions, and to determine whether the deletion interacts with the Fusarium head blight resistance gene.
A related project seeks to determine how this deletion impacts agronomic properties of wheat. Elite wheat genotypes from university colleagues have been used to introduce the deletion into them for this study. A greenhouse seed increase of this germplasm was completed, and the grain will be planted in the next fiscal year at an off-season nursery either in Arizona or in New Zealand to obtain sufficient quantities of grain to permit field plot plantings for the study in the next fiscal year. A new related project was initiated with an ARS colleague in North Dakota to evaluate the effect of the deletion on milling and baking quality of wheat grain. Three biological replicates of two nearly identical wheat genotypes that differ primarily by the presence or absence of the deletion were grown in the greenhouse in the current fiscal year and the seed was sent to the collaborator to use in comparative quality analyses.
A second area of research being pursued 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 transgenic plants that have one of the target genes for the project disrupted by a common gene editing method. The initial gene editing events were found to have been inherited in the following generation. Potential transgenic plants in which two separate susceptibility genes are being targeted for gene editing disruption have been recovered and later this FY will be evaluated for evidence of gene editing events in them. In parallel, research was undertaken to develop an efficient transformation method for oats, which will be needed to translate positive findings from Brachypodium to this crop species. A new oat genotype that is known to regenerate well from tissue culture conditions was obtained and used for this research. 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 found, and the overall frequency of transformation was found to be high, based on transient expression of a marker gene. Transformed embryos and callus tissue are now on a selective culture medium to favor selective growth of transformed cells, and later in the FY this material will be moved to a different medium to induce transgenic plant development from the transformed cells.
Lastly, the final stage of the coordination of the 2018 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 2019 Hard Red Spring Wheat Uniform Regional Performance Nursery, including development of a new 5-year material transfer agreement, developing the list of germplasm entries for this year’s evaluations, and organizing seed distribution to the program’s location cooperators, were completed.
Accomplishments
1. Identifying chromosomal locations of genes associated with vitamin B6 accumulation. Cereal grains are an important source of carbohydrates and other nutrients, including minerals and vitamins, for human diets. ARS researchers at Saint Paul, Minnesota, in collaboration with Japanese collaborators, used the model grass Brachypodium distachyon, a wild relative of wheat and rice, to identify the chromosomal locations of genes that contribute to the abundance of various metabolic compounds in seeds, including two associated with vitamin B6 metabolism. These results may lead to new strategies for vitamin B6 biofortification of grain crops to improve human health.
Review Publications
Della Coletta, R., Hirsch, C.N., Rouse, M.N., Lorenz, A., Garvin, D.F. 2019. Genetic dissection of nonhost resistance to wheat stem rust in Brachypodium distachyon. Molecular Plant-Microbe Interactions. 32(4):392-400. https://doi.org/10.1094/MPMI-08-18-0220-R.
Ondo, Y., Sawada, Y., Shimizu, M., Takahagi, K., Uehara-Yamaguchi, Y., Hirai, M., Garvin, D.F., Mochida, K. 2019. Identification of a putative pyridoxamine 5'-phosphate oxidase gene linked with 4-pyridoxate accumulation in seeds of Brachypodium distachyon through metabolite quantitative trait locus mapping. International Journal of Molecular Sciences. 20(9):2348. https://doi.org/10.3390/ijms20092348.
