Location: Plant Science Research
Project Number: 5062-30100-001-000-D
Project Type: In-House Appropriated
Start Date: Oct 1, 2024
End Date: Sep 30, 2029
Objective:
Objective 1: Deliver useful information on agronomic performance and scab resistance of elite hard red spring wheat to research, breeding, and grower stakeholders through improved operational efficiency and genetic methodologies.
Sub-objective 1.A: Coordinate the Hard Red Spring Wheat Uniform Regional Nursery (HRSWURN) and Uniform Regional Scab Nursery (URSN).
Sub-objective 1.B: Analyze data output from the HRWSURN and URSN to enable improvement of nursery design and quantify genetic diversity over the history of the HRSWURN and URSN.
Objective 2: Identify genomic regions in domestic wheat and oat and/or wild ancestors associated with biotic and abiotic stress tolerance.
Sub-objective 2.A: Enrichment sequencing of genomic loci associated with biotic stress resistance to identify genetic and epigenetic variation and guide wheat and oat breeding programs.
Sub-objective 2.B: Determine DNA methylation and gene expression profiles during plant infection to identify cell-type specific gene expression profiles associated with resistance that can be integrated into breeding programs.
Sub-objective 2.C: Develop a cell-based assay for high-throughput screening of pathogen effector protein recognition by diverse wheat and oat cultivars to accelerate discovery of novel disease resistance genes.
Objective 3: Develop novel genomic-enabled strategies for breeders to introduce and track genomic loci associated with improved performance.
Sub-objective 3.A: Develop more efficient marker-based identification of FHB resistance loci.
Sub-objective 3.B: Determine diversity at a wheat Xtu susceptibility gene promoter.
Approach:
Wheat is the most widely grown crop worldwide and is a critical staple cereal for fulfilling human caloric needs and maintaining food security. Oat is a major cereal for livestock feed and an important heart-healthy grain for human diets. The U.S. is a major producer and net exporter of wheat, but it is a minor producer and major importer of oat. There is growing demand for domestic oat for food and emergency forage. Predictable and stable production of these small grains relies on the continued development of high-yielding, high-quality cultivars. Wheat and oat breeding programs will continue to work towards these goals; however, they are challenged by ongoing and emerging biotic and abiotic stresses. Addressing these challenges will require researchers to identify and fill knowledge gaps in the genetic and genomic contributors to stress tolerance as well as leveraging this data to develop improved breeding strategies.
To accomplish the goals of Objective 1, the existing model of uniform regional nurseries will be continued to allow breeders to test their elite germplasm across the spring wheat growing region. Data from nursery trials will be shared publicly annually to allow breeders to make advancement decisions. High throughput sequencing and meta-analysis of historical regional performance data enable studies of genetic gain and allele frequency changes over the nearly 100 year history of the spring wheat regional nursery program. Objective 2 will rely on a suite of genomic and molecular biology techniques to track and discover variation associated with disease resistance. An adaptive sequencing approach utilizing Oxford Nanopore Technologies long read sequencing devices will enable selective sequencing of regions of interest in the large and complex wheat and oat genomes. These data will be useful for determining the genetic architecture and mode of action of loci under identified QTL. DNA methylation determined with ONT sequencing will be used to determine the impact of dynamic DNA methylation on gene expression during stress. An isolation of nuclei tagged in specific cell types (INTACT) system with stress responsive promoters will be developed in wheat to allow separation of nuclei from stressed and unstressed plant cells with the goal of enriching dynamic DNA methylation and gene expression changes. Protoplast assays will be used to screen libraries of fungal and bacterial pathogen virulence factors to dissect plant-microbe interactions and. Objective 3 will utilize SNP chip sequencing of diverse wheat cultivars to determine genetic variation at Fusarium resistance loci to improve breeding markers. Additionally, a wheat diversity will be screened using PCR primers specific to a Xanthomonas disease resistance gene promoter. If sufficient diversity is not detected in natural populations, it will be generated using genome editing techniques targeting the relevant segment of the promoter.
