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ARS Home Southeast Area Raleigh, North Carolina Plant Science Research Research





- Brown-Guedira, Gina
- Cowger, Christina
- Plant Genetic Resources, Genomics and Genetic Improvement (301)
- Plant Diseases (303)

Research Project: **Location:
                            Plant Science Research** Project Number: 6070-22000-019-000-D
                        
                        Project Type: In-House Appropriated Start Date: Mar 7, 2023
                        
                        End Date: Mar 6, 2028 **Objective:**
                        
                        Objective 1. Identify and develop small grain germplasm with improved resistance to rusts, powdery mildew, Fusarium head blight, and necrotrophic pathogens, and with increased tolerance to environmental stress.
Sub-objective 1.A: Coordinate Eastern Regional Nursery program for soft and hard winter wheat, winter barley and winter oats.
Sub-objective 1.B: Develop wheat germplasm with resistance to stripe rust (YR), leaf rust (LR), stem rust (SR), and powdery mildew (PM).
Sub-objective 1.C: Develop wheat and barley germplasm with resistance to Fusarium head blight (FHB).
Sub-objective 1.D: Develop wheat germplasm with resistance to Septoria nodorum blotch (SNB).
Sub-objective 1.E: Combine large historical genotypic and phenotypic data sets to understand the role of phenology in adaptation of wheat to diverse production environments.

Objective 2. Accelerate the breeding cycle through development of improved high-throughput genotyping methods for marker-assisted selection and genomic prediction coupled with rapid inbreeding methodology and apply these new tools in development of small grains cultivars. 
Sub-objective 2.A: Enhance SRWW genomic resources for identification of important genes, QTL and haplotypes for use in wheat improvement.
Sub-objective 2.B: Develop haplotype-informed, cost-effective genotyping platforms that can be paired with a practical haplotype graph for trait mapping, marker-assisted and genomic selection.
Sub-objective 2.C: Identify and characterize new QTL for important traits in eastern winter wheat germplasm.
Sub-objective 2.D: Develop new eastern winter wheat germplasm using marker-assisted breeding and genomic selection.

Objective 3: Develop new wheat germplasm and cultivars with enhanced end-use characteristics for the eastern United States.
Sub-objective 3.A: Develop new hard wheat cultivars with improved yield, disease resistance, and bread-making.
Sub-objective 3.B: Investigate the genetic basis of bread-making quality traits within the NC ARS hard wheat breeding program and develop breeding strategies that optimally make use of marker information for improvement of quality traits.

Objective 4. Determine commercially relevant diversity of Fusarium head blight (FHB) causing pathogens in eastern U.S. small grain crops, and provide research-based recommendations on fungicide applications to reduce FHB. 
Sub-objective 4.A: Determine commercial relevant diversity of Fusarium head blight (FHB) causing pathogens in eastern U.S. small grain crops.
Sub-objective 4.B: Provide research-based recommendations on fungicide applications to reduce FHB. **Approach:**
                        
                        1a. Distribute seed of regional nursery entries of winter wheat, winter barley and winter oats. Collate data, analyze and distribute reports.

1b. Cross elite, adapted lines with sources of seedling and adult plant resistance to stripe rust, leaf rust, stem rust, and powdery mildew. Coordinate identification of resistant lines in field breeding nurseries evaluated throughout the southeastern United States. Use reliable molecular markers for known resistance genes.

1c. Use inoculated, misted screening nurseries to evaluate regional and in-house breeding materials. Apply genomic selection models for scab resistance traits.

1d. Conduct appropriate phenotyping of regional and in-house breeding materials, including mapping populations, in inoculated Stagonospora blight nurseries to assist in locating the genes and associated markers to allow for marker-assisted selection.

1e. Develop models based on large historical genotypic and phenotypic data sets to understand the role of phenology in adaptation of wheat to diverse production environments.

2a. Assemble and annotate genomes of eastern wheat cultivars using long read sequencing and RNAseq analyses. New assemblies will be used for alignment in genotyping.

2b. Identified sequence variants from exome capture and genotyping by sequencing will be used to identify haplotypes in eastern germplasm. Practical haplotype graph will be used to inform development of targeted genotyping approaches and integrate information from multiple sequencing platforms.

2c. QTL mapping will be done using linkage maps for bi-parental mapping populations that are phenotyped traits in 1d.

2d. DNA markers will be assessed on parents and progeny under selection for marker-assisted and genomic selection. Selected lines will be advanced by project SYs and by collaborating brewing programs.

3a & 3 b. Each year, approximately 600 crosses will be made to combine superior quality, yield, agronomic, and disease and insect resistance using recurrent parents from the program, as well as new sources of diversity. Utilize combinations of genomic selection and molecular markers with phenotypic selection and screening to accumulate favorable agronomic traits. Phenotyping and selection for improved hard wheats lines; grow and select populations at multiple locations.

4a. Scabby wheat spikes will be collected from fields across as many eastern U.S. states as possible. Isolates will be purified and identified to species and chemotype determined. Population genetic analysis will be done.

4b. A multi-year field experiment in misted, inoculated FHB nursery will be done using three winter barley cultivars with different levels of resistance to FHB. Ten fungicide treatments will be evaluated in a split plot design to compare product efficacy and treatment timings. Compare benefits of fungicide application, cultivar resistance, and the combination of the two in terms of yield, test weight, and DON reduction.


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