Location: Wheat Health, Genetics, and Quality Research
2020 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.
Under Sub-objective 1A, ARS scientists at Pullman, Washington, made significant progress in developing new cultivars of club wheat. The club wheat breeding line ARS09X492-6CBW was entered into regional extension variety trials and is a candidate for release in 2021, targeted to the higher precipitation zone in southeastern Washington and northeastern Oregon. In 2019, a technical collaboration was initiated with the Japanese Flour Millers Association, the Washington Grain Commission, the ARS, and Washington State University to evaluate new club wheat breeding lines and ensure that selections for end-use quality are meeting expectations for the Japanese market. In the second year of the collaboration, all new samples presented were acceptable to the market. Discussions about the meaning of specific quality tests are ongoing. This collaboration directly enhances the ability of ARS scientists to meet Japanese quality targets and meet the needs of this important export market.
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, an important gauge of wheat grain quality. Low falling number is caused by two physiological responses to the environment. Resistance to preharvest sprouting, due to rain at harvest that causes the mature grain to germinate on the spike prior to harvest, was evaluated in wheat breeding lines and segregating populations using spike wetting tests. The other cause of low falling number is production of the enzyme alpha amylase during grain filling. Resistance to this late-maturity alpha-amylase was evaluated in multiple wheat cultivars and genotypes by inducing alpha amylase during grain fill using a cold treatment. The rankings of genotype response to these screens for the causes of low falling number were provided to wheat breeders in the Pacific Northwest.
For Sub-objective 1C, ARS scientists at Pullman, Washington, developed data management and analysis methods for high throughput phenotyping used in controlled environment studies. These techniques were applied to multiple projects including the analysis of root growth in wheat seedlings with differential tolerance to Rhizoctonia, the analysis of fireblight symptoms on apples, methods of quantifying spores and chlorosis on wheat leaves infected with stripe rust, analysis of wheat kernel morphology and color, and analysis of aluminum tolerance in wheat seedlings.
Significant progress was also made in Sub-objective 2A. ARS scientists at Pullman, Washington, evaluated 2757 breeding lines from 18 different public and private breeding programs located throughout the United States, at two locations in Washington and provided resistance data in July to all cooperators. Five recombinant inbred line populations that were segregating for resistance to stripe rust were evaluated for resistance and data reported to collaborators so that they could determine the genetic control of stripe rust resistance in their populations. Resistance was also rated on all major cooperative nurseries.
For Sub-objective 2B, ARS scientists at Pullman, Washington, rated the ‘D-genome Nested Association Mapping (DNAM) hard winter wheat population for resistance to stripe rust and confirmed that it possesses high temperature adult plant resistance and a potentially novel source of resistance to cereal cyst nematode. The DNAM was developed in collaboration with scientists at Michigan State University and Washington State University from a cross between a hard-white winter wheat from the great plains and multiple accessions of Aegilops tauschii.
For Sub-objective 2C, ARS scientists at Pullman, Washington, incorporated multiple genes for adult plant resistance to stripe rust into breeding lines targeted to regions in the United States where stripe rust is a threat to production. Because the stripe rust epidemic was light in 2019, selected lines were evaluated for a second year in 2020. Selections have been made and will be returned in the fall of 2020 to wheat breeders in Colorado, Oklahoma, Georgia, Illinois, and Nebraska.
For Sub-objective 3A, ARS scientists at Pullman, Washington, investigated the genetic architecture of response to freezing in a large panel of adapted soft white winter wheat. Previously identified loci associated with the vernalization and frost responsive genes on chromosome 5A, plus loci on chromosome 1A, 2A, 5B and 7B have been associated with frost tolerance in this population. This research identified a set of molecular markers that can increase winter survival in wheat.
For Sub-objective 3B, ARS scientists at Pullman, Washington, made progress in identifying the mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting. Work towards cloning the Enhanced Response to ABA-8 (ERA8) allele which provides increased sensitivity to the dormancy hormone Abscisic Acid (ABA) continued and current markers for this allele were used to introgress it into adapted winter and spring wheat breeding lines. Breeding lines possessing these markers were advanced in the field and will be harvested in 2020 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. ARS researchers in Pullman, Washington, screened two biparental populations for the late-maturity alpha-amylase phenotype in order to determine the genetic architecture of the trait in adapted germplasm. 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 4A, ARS researchers in Pullman, Washington, conducted exome capture, (sequencing of the protein coding genes in the wheat genome) on wheat breeding lines and cultivars contributed by regional breeders and distributed the results.
For Objective 4B, ARS researchers in Pullman, Washington, developed a pipeline that enhances the efficiency of 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.
For Objective 4C, ARS researchers in Pullman, Washington, coordinated the Western Regional Cooperative Nurseries which were grown at multiple locations in the Pacific Northwest. The nurseries were sent for disease screening for leaf and stem rust at the Cereal Disease laboratory and in Kenya, Africa. Data was reported on the unit web-site and shared via email as soon as it was available. ARS scientists in Pullman, Washington, assayed molecular markers of importance to regional public and private sector breeders on the Western Regional Nurseries. 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. Susceptibility to late-maturity alpha-amylase is a likely cause of poor wheat end-product quality in U.S. wheat. Farmers receive large discounts for wheat grain with low falling number, an indicator of starch breakdown. The production of late-maturity alpha-amylase during grain fill is one cause of low falling number. ARS researchers in Pullman, Washington, with collaborators at Washington State University, investigated the genetic control of late-maturity alpha-amylase production over multiple environments in a panel of 250 spring wheat varieties representing 10 North American breeding programs. 79% of genotypes showed susceptibility to late-maturity alpha-amylase. Resistance was associated with two loci previously mapped in Australian germplasm. These results indicate that late-maturity alpha-amylase is a major cause of low falling number in U.S. wheat and identified germplasm and molecular markers that are useful for development of wheat varieties with resistance.
2. Cultivars with stable high resistance to low falling number identified in northwestern U.S. winter and spring wheat cultivars. The falling number test is a standard method to assess end use quality in the grain trade. While ARS researchers have performed falling number tests on the multiple wheat varieties over multiple environments since 2013, summarizing these results was difficult because individual varieties were not included in all years or locations. ARS researchers in Pullman, Washington, with collaborators at Washington State University, used the factor-analytic statistical model to analyze data collected from 2013 to 2016. This approach compensated for the unbalanced nature of the dataset, allowing identification of varieties with stable falling number over multiple years and locations. These variety rankings have been shared through Washington State University extension with farmers and the grain industry to inform their selection and handling of wheat varieties, reduce discounts for poor quality grain and improve the grain industry’s ability to meet export market specifications.
3. New diversity available for the D-genome of wheat in the ‘DNAM’ population. Over 8,000 years ago, hexaploid (bread) wheat evolved via hybridization between tetraploid wheat and a small set of the wild diploid wheat, Aegilops tauschii spp. strangulata. The variability of the D-genome of wheat is much less that of the A and B genomes due to this bottleneck, and the lack of variability can make it difficult to improve wheat for certain traits like pest resistance and grain quality. ARS researchers in Pullman Washington, together with collaborators at Michigan State University and Washington State University, developed and characterized a D-genome nested association mapping panel comprising multiple and diverse Aegilops tauschii accessions crossed to an adapted hard white breeding line from the great plains. Novel resistance to stripe rust and to cereal cyst nematodes has been discovered in this population which has been released and deposited in the National Small Grains Collection for plant geneticists and breeders to access.
