Location: Plant Science Research
2024 Annual Report
Objectives
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.
Progress Report
In support of Objective 1, ARS researchers at Raleigh, North Carolina continued with work to develop superior small grain germplasm that is well adapted to the eastern United States. Our Eastern Uniform Regional Nursery program worked with 80 collaborators across 14 states to collate data, analyze and distribute reports for approximately 1,200 different lines of hard and soft red winter wheat, winter barley, and winter oats last season. In North Carolina, we planted at three locations and screened more than 7,700 plots for phenotypic and disease data. We also analyzed and gathered quality data from over 2,000 winter wheat and winter barley plots.
To address the threat of the Hessian fly (HF) to wheat production in the southern United States (US) and in response to stakeholder concerns, we have included HF resistance as a target in Sub-objective 1b. As part of this work, we have crossed wheat lines that possess known HF resistance genes to locally adapted varieties of soft red winter wheat; these HF genes are novel to the southeastern U.S. and will aid in building and maintaining resistance to HF. Additionally, we have crossed adapted wheat varieties that are resistant to wheat rust, head scab, and powdery mildew to distribute resistant germplasm to southeastern wheat breeders.
We have continued working to isolate the gene underlying a locus for field resistance to HF that was previously identified by our group. Collaborative analysis with breeding programs demonstrated the importance of the locus located on chromosome 7D in providing field resistance at multiple US locations. Plants from a near-isogenic population developed from the cross between the resistant line LA03136E71 and the susceptible cultivar Shirley were genotyped and seed harvested. This high-resolution mapping population will be evaluated at several locations across the southeastern United States to refine our knowledge of the underlying genetic mechanisms that govern this field tolerance.
In support of Sub-objectives 2a and 2b, long-read DNA sequences were obtained for multiple eastern soft winter wheat lines, including the Hessian fly resistant line LA03136E71. A robust pipeline was implemented to develop chromosome level genome assemblies and these assemblies are currently being thoroughly scrutinized to ensure quality control prior to publication.
To improve the utility of these assemblies, six different tissue types were collected, and RNA sequencing was done to support gene annotation of two of the sequenced wheat lines. A de novo gene annotation pipeline is currently under development and these de novo gene annotations will serve as the foundation for annotating all other sequenced lines in our possession. Work is ongoing to include these assemblies in a local pangenome of soft red winter wheat and our group plans to implement a practical haplotype graph using these wheat assemblies. These novel resources will aid in the identification of novel gene variations and causal genes for traits of interest. Moreover, these genomic resources are already leading to the identification of important gene variants.
In support of Sub-objective 2c, linkage maps were made in multiple bi-parental mapping populations. Quantitative trait locus (QTL) mapping identified genome regions associated with resistance to Fusarium head blight, powdery mildew, stripe rust, and Stagonospora blight. Fine mapping identified candidate genes underlying powdery mildew resistance gene Pm54 and stem rust resistance gene SrA2K. These genes are present in wheat cultivar AGS2000, for which we developed a genome assembly (Sub-objective 2a) critical to this work. Validation of the resistance genes and development of predictive marker assays is ongoing.
We conducted a genome-wide association study using 15 years of phenotypic and genotypic data from a panel of ~2300 wheat lines. We identified a QTL in the distal part of the short arm of chromosome 1B, associated with resistance to Stagonospora glume blotch. We also performed QTL analysis using a doubled haploid population developed from the cross between Catawba × NC-12-22844 and identified QTL for resistance to Stagonospora blotch and Fusarium head blight.
In support of Sub-objective 2d, more than 10,000 wheat, 500 barley and 400 oat lines provided by breeding programs were genotyped with genome-wide markers. Data were used by collaborating programs to develop models for predictive breeding. In addition, a new genotyping platform targeting 5,000 markers, including markers with known association with important traits, was developed and tested for wheat. Scripts were prepared that combine the output from different genotyping platforms and apply consistent calling criteria for reporting that is compliant with the USDA-ARS T3 database. These scripts were shared with other researchers. Additionally, approximately 1,000 doubled haploid lines were developed from high priority crosses for improvement of resistance to head scab and for gene mapping. Seed was provided to breeders for Fall 2024 planting.
In support of Objective 3, the small grain breeding program advanced 21 elite hard red winter wheat and winter barley lines into uniform nurseries for final evaluations to determine suitability for release as cultivars. We also made 160 new crosses of hard red winter wheat, 80 new crosses of malting winter barley, and 180 new crosses of winter oats.
We are expanding on our important “gene for genes” discovery, which was that wheat resistance gene Pm1a interacts with two powdery mildew effectors located on different chromosomes. Now there is strong evidence that one of those effectors or a gene just downstream of it also interacts with a different wheat powdery mildew resistance gene, Pm4. Investigating these dynamics is changing the way we understand the interactions of the products of wheat resistance genes and fungal effector genes. These interactions determine whether the wheat resistance genes are effective, and how durable they are likely to remain.
Accomplishments
1. Broadly effective field resistance to Hessian fly identified in wheat. The Hessian fly (HF) is an insect pest that feeds on wheat, causing significant reduction in yield. HF can cause economic disaster in regions with amenable climate and the production area under threat is expanding as warmer winters conducive to multiple life cycles of the insect lead to greater crop damage. Field resistance to the HF refers to the ability of wheat to tolerate infestation and this type of resistance is not detectable by greenhouse assays. Working with collaborators, ARS researchers at Raleigh, North Carolina conducted a study to evaluate HF infestation at multiple field locations for a population of wheat developed from a cross between an adapted breeding line having field resistance with a susceptible line. We were able to identify DNA markers associated with a locus responsible for field resistance. Evaluation of thousands of new breeding lines with DNA markers and field testing at locations in Texas, Louisiana and Georgia indicate that this resistance locus is widely effective. This work has identified a potentially novel type of HF resistance that is a target of further study. The new DNA markers are being deployed to track this resistance locus as it is immediately useful to breeders for developing improved HF resistant cultivars.
2. Identification of a gene in soft red winter wheat for resistance to Ug99 stem rust. Highly virulent races of the pathogen causing wheat stem rust presents a major challenge to global wheat production. Growing resistant varieties is the most economically feasible method of disease control and wheat breeders strive to develop lines having more than one resistance gene to increase durability. Reliable DNA markers that allow tracking of resistance genes are needed for deployment strategies to combat highly virulent pathogen races. In this study, ARS researchers at Raleigh, North Carolina used populations derived from two soft red winter wheat lines to locate a resistance gene to the short arm of wheat chromosome 6D where Sr resistance genes Sr42, SrCad, and SrTmp have been identified. We exploited new DNA sequencing data to enrich the region around the gene and developed a predictive DNA marker. Evaluation of our new DNA assays demonstrate that they can be used to track this Sr resistance in breeding programs. This research will help wheat breeders develop improved cultivars having multiple genes for resistance to stem rust, thus improving durability of resistance.
3. Novel method created to identify and quantify diverse Fusarium species. In cereal grain samples affected by Fusarium head blight, it is difficult to determine whether multiple Fusarium species are present and how much of each is present, yet this information is important for detecting mycotoxins. ARS researchers at Raleigh, North Carolina undertook a study to create a new method for quantifying the absolute abundances of multiple Fusarium species in samples ranging from individual cereal heads to pooled grain samples from individual fields. This study created a method called synthetic spike-in metabarcoding (SSIM) that can accurately and precisely quantify multiple Fusarium species co-inhabiting wheat samples across a wide range of pathogen concentrations. The method has an advantage over previous methods in that species-specific primers are not used, so detectable Fusarium species are not limited to those for which species-specific primers are available. Samples can be directly compared not only for Fusarium species present, but also absolute abundance of each species. This information is useful to determine which mycotoxins may be present in a sample.
4. Septoria nodorum blotch (SNB) ratings provided to 17 breeding programs. Entries in seven regional nurseries were planted together with standard SNB-resistant and -susceptible checks. A total of 381 advanced experimental lines were evaluated at two North Carolina locations, with two replicates of each entry at each location. SNB severity was enhanced through wheat straw inoculation and irrigation. High-quality data on glume and foliar SNB severity were produced and shared with breeders, who would otherwise not have been likely to obtain SNB ratings of their materials, especially due to the very dry spring. The data were statistically analyzed and ready to be used in cultivar release publications.
Review Publications
Ballén-Taborda, C., Lyerly, J., Smith, J.H., Howell, K.D., Brown Guedira, G.L., Dewitt, N., Ward, B., Babar, M., Harrison, S.A., Mason, R.E., Mergoum, M., Murphy, J., Sutton, R., Griffey, C.A., Boyles, R.E. 2024. Predicting superior crosses in winter wheat using genomics: A retrospective study to assess accuracy. Crop Science. 64(4):2195-2211. https://doi.org/10.1002/csc2.21266.
Dewitt, N., Lyerly, J., Guedira, M., Holland, J.B., Murphy, J., Ward, B.P., Boyles, R.E., Mergoum, M., Babar, M., Shakiba, E., Ibrahim, A., Tiwari, V., Santantonio, N., Van Sanford, D., Harrison, S.A., Brown Guedira, G.L. 2023. Bearded or Smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States. Journal of Experimental Botany. 74(21):6749-6759. https://doi.org/10.1093/jxb/erad318.
Boyles, R., Dewitt, N., Winn, Z., Murphy, P., Cowger, C., Costa, J., Saripalli, G., Tiwari, V., Ballen-Taborda, C., Lyerly, J., Mergoum, M., Brown Guedira, G.L., Santantonio, N., Johnson, J., Mason, R., Sutton, R., Ibrahim, A., Harrison, S., Griffey, C., Marshall, D., Van Sanford, D. 2024. Approaching 25 years of progress toward Fusarium head blight resistance in southern soft red winter wheat (Triticum aestivum L). Plant Breeding. 143(1):66-81. https://doi.org/10.1111/pbr.13137.
Burridge, A.J., Winfield, M., Przewieslik, A., Edwards, K.J., Siddique, I., Barral-Arca, R., Griffiths, S., Cheng, S., Huang, Z., Feng, C., Dreisigacker, S., Bentley, A.R., Brown Guedira, G.L., Barker, G.L. 2024. Development of a next generation SNP genotyping array for wheat. Plant Biotechnology Journal. 22(8):2235-2247. https://doi.org/10.1111/pbi.14341.
Babar, M., Khan, N., Blount, A., Barnett, R.D., Harrison, S.A., Dewitt, N., Johnson, J., Mergoum, M., Boyles, R., Murphy, P., Mason, E., Shakiba, E., Ibrahim, A., Sutton, R., Brown Guedira, G.L., Marshall, D., Cowger, C., Baik, B.V., Santantonio, N., Cambron, S.E., Jin, Y., Mailhot, D. 2024. Registration of FL16045-25: An early-maturing, high-yielding, disease-resistant soft red facultative wheat variety for the Southern U.S.. Journal of Plant Registrations. 18(2):374-387. https://doi.org/10.1002/plr2.20343.
