Location: Wheat Health, Genetics, and Quality Research
2019 Annual Report
Objectives
The long-term objective of this project is to improve the resilience of wheat plants under environmental stress. Specifically, during the next five years we will focus on the following objectives.
Objective 1. Genetically improve soft white winter and club wheat for environmental resilience, disease resistance, and end-use quality.
Subobjective 1A: Develop and release club (Triticum aestivum ssp. compactum) wheat cultivars with resistance to major regional diseases and adaptation to diverse environments in the western U.S.
Subobjective 1B: Select breeding lines with better end-use quality and high Falling Numbers (FN) due to preharvest sprouting (PHS) and late maturity alpha-amylase (LMA) resistance.
Subobjective 1C: Select soft white wheat breeding lines using indirect selection based on high throughput phenotyping (HTP) targeted to specific combinations of climate variables.
Objective 2. Identify genetic resources and introgress multiple genes for resistance to stripe rust and to soil borne diseases into wheat germplasm.
Subobjective 2A: Identify novel genetic resources with resistance to stripe rust and soil borne disease and identify loci controlling this resistance.
Subobjective 2B: Introgress novel sources of resistance to stripe rust and soil borne disease from landraces into adapted wheat germplasm.
Subobjective 2C: Conduct collaborative pre-breeding to introgress disease resistance from multiple germplasm accessions into adapted germplasm.
Objective 3. Develop, evaluate, and use genotyping technologies and sequence information to increase knowledge of basic genetic processes controlling environmental resilience, disease resistance, and end-use quality in wheat and barley.
Subobjective 3A: Identify genetic and molecular mechanisms that regulate response to low temperatures.
Subobjective 3B: Identify genetic and molecular mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting.
Subobjective 3C: Identify genetic and molecular mechanisms causing late-maturity alpha amylase expression during grain development.
Subobjective 3D: Identify genetic mechanisms for resistance to disease.
Objective 4. Incorporate genomic data in wheat and barley selection strategies by collaborating with regional breeding programs.
Subobjective 4A: Develop molecular methods for use in genome wide association (GWAS), genomic selection, and transcriptomic strategies to evaluate wheat and barley germplasm.
Subobjective 4B: Develop bioinformatic pipelines to facilitate use of genomic data in wheat and barley improvement.
Subobjective 4C: Provide genomic and phenotypic data to Western Regional and U.S. Wheat and Barley improvement programs.
Approach
Subobjective 1A: Doubled haploids, genomic selection, and high throughput phenotying are used to increase gains from selection targeted to dry or high rainfall environments in the USDA-ARS club wheat breeding program.
Subobjective 1B: Selection for preharvest sprouting and late maturity alpha-amylase resistance based on phenotypic and genotypic data identifes wheat breeding lines with stable high falling number. Tools and tests are developed to detect low falling number wheat, and to distinguish between late maturity alpha amylase and preharvest sprouting. Controlled environment and field-based screening systems are optimized. Plant genetic, biochemical and physiological components associated with low falling numbers are investigated, including the protein biochemistry of alpha amylase, and hydrolytic enzymes expressed during wheat grain development and gation.
Subobjective 1C: Genomic selection, high throughput phenotyping and meta-environmental analylsis are used to increase the accuracy breeding program data. Genome estimated breeding values are calculated for soft white and club wheat.
Subobjectives 2A and 2B: Dominant male sterility, marker-assisted selection and phenotypic selection are used to incorporate new sources of resistance to stripe rust and to soil borne disease into adapted backcross populations of wheat.Subobjective 2C: F4 bulk populations are developed and selected for adult plant resistance to stripe rust in collaboration with U.S. wheat breeders, followed by selection for agronomic traits and re-evaluation for resistance.
Subobjective 3A: Genes, identified from expression studies that contribute to low temperature tolerance, are combined to increase the level of low temperature tolerance in wheat.
Subobjective 3B: Preharvest sprouting resistance is increased when mutant alleles associated with altered hormone sensitivity are combined to provide increased seed dormancy. Markers linked to emergence traits are developed.
Subobjective 3C: A genome wide association study for resistance to late maturity alpha amylase is conducted, near isogenic lines differing for susceptibility loci are developed and breeding populations are screened in collaboration with wheat breeders.
Subobjective 3D: The functional gene for stripe rust resistance is identified using a knock out of that resistance in an EMS-mutagenized population.
Subobjective 4A: Targeted amplicon sequencing of at least 1500 known informative markers that are important for selection in western U.S. breeding programs is used to genotype breeding lines.
Subobjective 4B: Software tools are developed to apply genomic data to crop improvement.
Subobjective 4C: Genomic and phenomic data are provided to public and private sector participants in the Western Regional Cooperative Nurseries and the Western Regional Small Grains Genotyping Laboratory.
Progress Report
This report documents progress for project 2090-21000-033-00D, entitled “Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality”, which started in March 2018. Progress was made on all four Objectives, which fall under National Program 301, Component 1, Crop Genetic Improvement, and Component 3, Crop Biological and Molecular Processes. Progress on this project focuses on Problem Statement 1A: Trait discovery, analysis, and superior breeding methods; Problem Statement 1B: New crops, new varieties, and enhanced germplasm with superior traits; and on Problem Statement 3A: Fundamental knowledge of plant biological and molecular processes.
Under Sub-objective 1A, ARS scientists at Pullman, Washington, made significant progress in developing and releasing new cultivars of club wheat. The new cultivar, ‘Castella’, was increased as breeder seed. Castella possesses excellent grain yield, excellent end use quality for cake and cookie baking and combined seedling and adult plant resistance to stripe rust and has strong interest from seed dealers in Washington State. In addition, several promising new club wheat breeding lines were entered into statewide performance trials in Oregon, Idaho and Washington. As the only club wheat breeding program in the world, the ARS breeding program supplies the raw product for a significant component of the export wheat market in the Pacific Northwest.
Under Sub-objective 1B, ARS scientists at Pullman, Washington, made significant progress in selecting wheat breeding lines with better end-use quality and high falling numbers by combining resistance to preharvest sprouting with late maturity alpha-amylase resistance. Data from spike wetting screens for resistance to preharvest sprouting and from induced late maturity alpha amylase screens were collected from advanced soft white breeding lines and provided to wheat breeders in the Pacific Northwest. Segregating populations and regional nursery germplasm were screened for previously identified molecular markers associated with preharvest sprouting and were also assayed for falling numbers to validate markers in Pacific Northwest germplasm.
For Sub-objective 1C, ARS scientists at Pullman, Washington, conducted the final year of three of evaluation of several high-throughput field phenotyping techniques on a segregating population of winter wheat under drought and well-watered environmental conditions in Colorado, Oregon, and Washington. Plant biomass data were collected via aerial drone flights at 200-300 feet in order to correct for spatial variability in field plot trials. Data management and analysis methods for high throughput phenotyping were evaluated and used in controlled environment studies.
Significant progress was made in Sub-objective 2A. In order to identify new sources of resistance, ARS scientists at Pullman, Washington, assayed a subset of the DNAM (a synthetic hexaploid nested association mapping (NAM) population) for seedling and adult plant resistance in the greenhouse to identify novel stripe rust resistance in the D-genome. Further resistance screenings will be done on this population in FY19 and on landrace lines from the other wheat populations. Synthetic wheat populations derived from CIMMYT winter synthetic wheat breeding lines were screened for resistance using stripe rust races Pstv-37 and Pstv-51. ARS scientists at Pullman, Washington, evaluated two,005 breeding lines from 19 different public and private breeding programs located throughout the U.S. at two locations in Washington, and provided resistance data in July to all cooperators. Seedling resistance to stripe rust was rated on 1307 breeding lines from the southern U.S. and rated resistance for all major cooperative nurseries.
For Sub-objective 2C, ARS scientists at Pullman, Washington, incorporated multiple genes for adult plant resistance to stripe rust into breeding lines that are nominated by other breeders from the U.S. Resistant heads from BCF3 populations were returned to breeders and a sample was kept for validation in 2018. Approximately 184 BC1F4 heads selected from field screening of BC1F3 populations were return to wheat breeders in Colorado, Oklahoma, Georgia, Illinois, and Nebraska.
For Sub-objective 3B, ARS scientists at Pullman, Washington, are working to identify the mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting. Molecular markers were identified that are linked to the ENHANCED RESPONSE TO ABA8 (ERA8) allele which provides increased sensitivity to the dormancy hormone ABA and improved resistance to low falling numbers. Breeding lines possessing these markers were advanced in the field and will be harvested in 2019 to confirm their usefulness in breeding.
Progress was made on Sub-objective 3C to identify the genetic and molecular mechanisms causing late-maturity alpha amylase expression during grain development in spring and in winter wheat. One spring wheat and one winter wheat association mapping panel were screened for the late-maturity alpha amylase phenotype for the second year in the greenhouse and in the field. Additionally, biparental populations were screened for the late-maturity alpha amylase phenotype in order to identify useful populations that are segregating for the late-maturity alpha amylase trait. Progeny from crosses between resistant and susceptible parents were advanced to develop near isogenic lines differing for specific susceptibility loci so that the effect of each locus can be determined.
For Objective 4, ARS researchers in Pullman, Washington, developed and refined the Targeted Amplicon Sequencing (TAS) approach to genotyping for wheat and barley that provides increased numbers of data points per sequencing lane, identifies segregation for major known loci of importance to wheat breeders and simplifies the post processing of sequencing data. The scientists coordinated the Western Regional Cooperative Nurseries which were grown at multiple locations in the Pacific Northwest. Data was reported on the unit web-site and shared via email. The nurseries were also sent for disease screening for leaf and stem rust at the Cereal Disease laboratory and in Kenya, Africa. ARS scientists in Pullman, Washington, assayed molecular markers of importance to regional public and private sector breeders on the Western Regional Nurseries and reported data. These services aid regional breeders in maintaining the efficiency and high quality of their breeding programs so that productive wheat cultivars are available for farmers to grow.
Accomplishments
1. New statistical methodology identifies wheat cultivars with stable high falling numbers. Statistical methods for separating genetic and environmental effects were applied to a large dataset of falling numbers data collected over five years. Northwest farmers lost approximately $200 million to discounts due to low falling numbers in 2016. ARS researchers and collaborators at Washington State University in Pullman, Washington, examined the utility of statistical methods to identify resistant varieties based on over 15,000 falling numbers datapoints from testing of state extension variety trials performed since 2013. The results allow wheat breeders and farmers to identify varieties that had more stable higher falling numbers over many years and locations.
2. A new club wheat, Castella, is released for the intermediate rainfall region of Washington state. ARS scientists in Pullman, Washington, developed and released Castella club wheat, which is resistant to stripe rust, aluminum, and hessian fly, and possesses excellent club wheat end use quality. Club wheat is a significant part of the wheat export market in the Pacific Northwest, but current club wheat cultivars are either susceptible to low falling numbers, or susceptible to stripe rust. A combination of single seed descent, marker assisted selection and multi-location field trials was used to develop Castella club wheat from a cross with a diverse pedigree including breeding lines from Washington, New York, and Arkansas. This diverse pedigree has resulted in an unusual combination of traits in Castella that increase marketing opportunities for growers.
3. Two molecular markers are effective screening tools for seedling and adult plant resistance to stripe rust in Pacific Northwest germplasm. Two molecular markers, the YR17-SNP marker and a new marker, Yr_IWB12603, are being used to select for seedling and adult plant resistance to stripe rust (also known as yellow rust (Yr)). Although several molecular markers have been identified for stripe rust resistance, their use is limited in soft wheat breeding programs. ARS researchers in Pullman, Washington, examined several combinations of molecular markers in the ARS wheat breeding program and associated these with seedling and adult plant stripe rust resistance based on greenhouse and field trials. The SNP marker, Yr_IWB12603, for the QYr.wac-1B.1/Qyr.wpg-1B.2/ QYrMa.wgp-1BS locus on chromosome 1B is likely a new combination of genes for seedling and adult plant resistance in the same region as several other stripe rust resistance (Yr) genes. The use of these two markers provides an alternative to the use of markers associated with the stripe rust genes Yr5 and Yr15 and will increase the frequency of combined adult plant and seedling resistance to major stripe rust races.
4. The regulation of the plant hormone gibberellic acid, which is critical in seed dormancy and crop emergence, is highly specialized. The ‘GID1’ gibberellic acid (GA) receptors can both positively and negatively regulate seed germination. Mechanisms controlling seed dormancy and crop emergence, major factors determining preharvest sprouting resistance and yield, are not well understood. The plant hormone GA stimulates germination and seedling emergence, leading to an assumption that the GA receptors should also stimulate germination. ARS researchers in Pullman, Washington, used mutant analysis in Arabidopsis to learn that the ‘GID1c’ receptor stimulates germination, the ‘GID1b’ receptor represses germination, and the ‘GID1a’ receptor can both positively and negatively regulate germination in the dark. This reveals that GA receptor function can be highly specialized and are interesting targets for controlling preharvest sprouting and emergence.
5. A method of evaluating late maturity alpha amylase (LMA) in the field is developed to facilitate breeding for reduced LMA. A field-based late maturity alpha amylase (LMA) testing system was developed. Over half of northwestern winter wheat cultivars are susceptible to LMA, a problem that caused major losses due to low falling numbers in several years since 2012. ARS researchers in Pullman, Washington, developed a field LMA testing system and used this method to screen hundreds of wheat breeding and germplasm for LMA susceptibility. This work enabled wheat breeders to select against LMA susceptibility in their breeding programs.
6. Antibodies to specific wheat alpha amylase enzymes are developed for use in development of rapid assays for low falling numbers in wheat. Monoclonal antibodies to wheat alpha-amylase were raised. Problems with low falling numbers can result from either preharvest sprouting (the germination of mature grain on the mother plant) or a cold-induced defect during grain development called late maturity alpha-amylase (LMA). ARS researchers and Washington State University researchers in Pullman, Washington, raised monoclonal antibodies that specifically recognize wheat TaAmy1 or TaAmy1 and TaAmy2. These results enable the development of ELISA assays for wheat preharvest sprouting and LMA.
Review Publications
Ibba, M., Kiszonas, A., See, D.R., Skinner, D.Z., Morris, C.F. 2018. Mapping kernel texture in a soft durum (Triticum turgidum ssp. durum) wheat population. Journal of Cereal Science. 85:20-26. https://doi.org/10.1016/j.jcs.2018.10.006.
Ando, K., Krishnan, V., Rouse, M.N., Danilova, T., Friebe, B., See, D.R., Pumphrey, M. 2019. Introgression of a novel Ug99-effective stem rust resistance gene into wheat and development of Dasypyrum villosum chromosome specific markers via genotyping-by-sequencing (GBS). Plant Disease. https://doi.org/10.1094/PDIS-05-18-0831-RE.
Qie, Y., Liu, Y., Wang, M., Li, X., See, D.R., An, D., Chen, X. 2018. Development, validation, and re-selection of wheat lines with pyramided genes Yr64 and Yr15 linked on the short arm of chromosome 1B for resistance to stripe rust. Plant Disease. 103(1):51-58. https://doi.org/10.1094/PDIS-03-18-0470-RE.
Liu, L., Wang, M.N., Feng, J.Y., See, D.R., Chen, X. 2019. Whole genome mapping of stripe rust resistance QTL and race-specificity related to resistance reduction in winter wheat cultivar Eltan. Phytopathology. 109(7):1226-1235. https://doi.org/10.1094/PHYTO-10-18-0385-R.
Ge, W., Steber, C.M. 2018. Positive and negative regulation of seed germination by the Arabidopsis GA hormone receptors, GID1a, b, and c. Plant Direct. 2(9):e00083. https://doi.org/10.1002/pld3.83.
Gizaw, S.A., Godoy, J.G., Garland-Campbell, K.A., Carter, A.H. 2018. Genome-wide association study of yield and component traits in Pacific Northwest winter wheat (Triticum aestivum L.). Crop Science. 58(6):2315-2330. https://doi.org/10.2135/cropsci2017.12.0740.
Sanad, M.N., Smertenko, A., Garland Campbell, K.A. 2019. Differential dynamic changes of reduced trait model for analyzing the plastic response to drought phases: a case study in spring wheat. Frontiers in Plant Science. 10:504. https://doi.org/10.3389/fpls.2019.00504.
Kiszonas, A., Higgenbotham, R., Chen, X., Garland-Campbell, K.A., Bosque-Perez, N.A., Pumphrey, M., Rouse, M.N., Hole, D., Wen, N., Morris, C.F. 2019. Agronomic traits in durum wheat germplasm possessing puroindoline genes. Agronomy Journal. 111(3):1254-1265. https://doi.org/10.2134/agronj2018.08.0534.
