Location: Wheat Health, Genetics, and Quality Research
2022 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 2090-21000-033-000D, 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 researchers in Pullman, Washington, made significant progress in developing new cultivars of club wheat. The new club wheat cultivar, ‘Cameo’ (previously identified as ARS09X492-6CBW) was proposed for release. Foundation seed was produced in collaboration with the Washington Crop Improvement Association and the line was entered into multi-state variety trials. There is strong interest in Cameo from local wheat growers and seed growers, over 10,000 pounds of grain have been requested. Cameo is targeted to northern Idaho, southeastern Washington, and northeastern Oregon. New club wheat breeding lines ARS12X097-12C and ARS09X500-17C were evaluated in statewide trials and will be retested in 2023. The fourth year of the club wheat technical collaboration between the USDA and the Japanese Flour Milling Association (JFMA) was held in July 2022. The purpose of the collaboration is to evaluate new club wheat breeding lines and ensure that selections are acceptable for end-use quality. All new club wheat breeding lines evaluated in 2022 met expectations for the Japanese market. This collaboration directly enhances the ability of ARS scientists to achieve the technical quality expectations this important export market.
Under Sub-objective 1B, ARS researchers in 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 numbers are caused by two physiological factors named preharvest sprouting and late maturity alpha amylase. Preharvest sprouting is due to rain at physiological maturity that causes the mature grain to germinate on the spike prior to harvest. Low falling numbers are also caused by production of the enzyme alpha amylase during grain filling. Resistance to preharvest sprouting was evaluated in wheat breeding lines and segregating populations using spike wetting tests. 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 two causes of low falling number were provided to wheat breeders and producers in the Pacific Northwest. A new 96 well plate assay for alpha amylase was developed making it easy to screen hundreds of samples.
For Sub-objective 1C, ARS researchers in Pullman, Washington, collaborated with scientists at Washington State University to collect high throughput image data on multiple field nurseries and are using it with genomic selection models to improve decision making in the breeding program.
Significant progress was also made in Sub-objective 2A. ARS researchers in Pullman, Washington, evaluated over 1800 breeding lines from 19 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. Resistance was also rated on all major cooperative nurseries. While stripe rust did not occur in much of the United States in 2022 due to the heat, cooperators were able to make use of these data from ARS researchers to make for their selections.
For Sub-objective 2B, ARS researchers in Pullman, Washington, evaluated a recombinant inbred population segregating for resistance to cereal cyst nematode with resistance derived from a D-genome parent used in the D-genome nested association mapping (DNAM) population. This is a novel source of resistance to cereal cyst nematode. ARS researchers also examined new germplasm for resistance to aluminum toxic soils if greenhouse and field screening trials conducted in Washington.
For Sub-objective 2C, ARS researchers in 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 of the drought in 2021, selected lines were retested in 2022 in Pullman, Washington, and then returned to breeders in fall of 2022.
For Sub-objective 3A, ARS researchers in Pullman, Washington, evaluated breeding lines and cultivars for resistance to freezing and reported data to the Washington State seed buyers guide.
For Sub-objective 3B, ARS researchers in Pullman, Washington, made progress in identifying the mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting. The Enhanced Response to ABA-8 (ERA8) allele which provides increased sensitivity to the dormancy hormone Abscisic Acid (ABA) was incorporated into spring wheat germplasm.
Progress was made on Sub-objective 3C in identifying the genetic and molecular mechanisms that cause late-maturity alpha-amylase expression during grain development in spring and in winter wheat. ARS researchers in Pullman, Washington, screened the Cara/Xerpha doubled haploid population for the late-maturity alpha-amylase phenotype and determined that the strongest resistance locus was closely linked to the C gene for club wheat. In another population, near isogenic lines differing for specific susceptibility loci were developed and are now in in the F-3 stage of development.
For Sub-objective 4A, ARS researchers in Pullman, Washington, conducted exome capture and promoter capture, (sequencing of the protein coding genes in the wheat genome) on a set of wheat breeding lines and cultivars contributed by regional breeders and distributed the results.
For Sub-objective 4B, ARS researchers in Pullman, Washington, developed a pipeline that enhances the efficiency of the genotype by multiplexed sequencing (GMS) 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. Multiple candidate regions or signals for positive selection were identified in state, regional, and market class populations. Further validation of these candidate regions in specific breeding programs may lead to identification of set of loci that can be selected to restore population-specific adaptation without multiple backcrossing which will facilitate the use of novel alleles from germplasm and landraces.
For Sub-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. Data was reported on the unit website 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. Development of environomic prediction to predict spring wheat performance. Changing climate conditions have profound impacts on crop performance from natural fields, but machine learning algorithms specifically designed to capture such impacts are scarce. ARS researchers at Pullman, Washington, in collaboration with researchers at Washington State University, University of Idaho, and Iowa State University, developed a novel machine learning algorithm, environomic prediction (EP), enabling the accurate forecast prediction of performance trend based on daily weather conditions. The potential of EP was demonstrated by six important traits (including yield and quality trait) from the Idaho variety testing trials spanning 16 years at five locations. This EP model can be used to forecast crop performance so growers will be able to adjust the management practices based on the prediction.
2. Plant UBX-domain containing protein 1 (PUX1) is a new gibberellic acid (GA) hormone signaling gene. The GA receptor GID1 controls all aspects of GA response in plants, but not all of its functions can be explained by interaction with DELLA proteins (a short stretch of amino acids that are known to regulate GA signaling). ARS researchers at Pullman, Washington, and colleagues at Washington State University, and the University of Wisconsin, identified PUX1 as a GID1-interacting protein and found that it acted via both DELLA-dependent and independent mechanisms to negatively regulate GA responses including seed germination, stem elongation, and the transition to flowering. These results fundamentally improve our understanding of how the GA hormone controls these responses which are essential to agricultural traits including preharvest sprouting tolerance, emergence, and earliness.
3. Development of a 96-well alpha-amylase enzyme assay. It is difficult to characterize late maturity alpha-amylase (LMA), the expression of alpha-amylase during grain maturation in response to cold temperatures, using the falling numbers test because it requires too much grain for the carefully staged single-spike LMA induction assays. ARS researchers at Pullman, Washington, and colleagues at Washington State University, developed a high throughput 96-well assay using the Phadebas chemistry allowing accurate screening in single-spike samples. This result will provide rapid screening for LMA and preharvest sprouting tolerance in wheat breeding programs that will facilitate selection for resistance to low falling numbers.
4. Loci, effective in resistance to Stripe Rust in U.S. wheat, identified. Stripe rust is a devastating global wheat disease and the hexaploid club spring wheat cultivar JD contains both all-stage and adult plant resistance but the genes controlling this resistance are unknown. A population derived from a cross between JD and a susceptible wheat was assayed in the field and a major gene for resistance was identified on the short arm of chromosome 1B and a marker, wmc708, was closely linked. Additional resistance genes were detected on chromosomes 3A, 3B, 4A, 6B, and 7A which, together contribute to resistance. This research provides molecular markers and targets to combine new genes for stripe rust resistance into other classes of wheat and will reduce grower dependence on fungicides to control this disease.
5. Genetic diversity in wheat has not declined; on the contrary, it actually seems to be slightly increasing. Wheat is a major human food crop and continued wheat improvement, and resilience depends on maintenance of genetic diversity. ARS researchers in Pullman, Washington, examined trends in genetic diversity in wheat cultivars released from the late nineteenth century until the present and discovered that population structure was defined by market class and that genetic diversity had not decreased after the release of the first semidwarf wheat varieties in 1961. In fact, diversity estimates have increased in several wheat market classes indicating that sufficient variation exists in wheat for continued genetic improvement to meet future needs.
6. Plant height determinants characterized. Understanding mechanisms underlying plant height, the iconic trait of the Green Revolution, has significant bearings on improving crops, however, how gene, environmental conditions, and development process, and their interaction in determining plant height are inter-connected remain unclear. ARS researchers in Pullman, Washington, in collaboration with researchers at Iowa State University identified the novel genetics controlling plant height and the explicit environmental condition (early season temperature) these plant height genes responded to, and then depicted how these two determinants interacted with the developmental process. The research outcome presented the first case of illustrating the plant height in the defined gene-environment-development three-dimension space and results in specific targets to match plant growth to optimal growing environments.
Review Publications
Mu, Q., Guo, T., Li, X., Yu, J. 2022. Phenotypic plasticity in plant height shaped by interaction between genetic loci and diurnal temperature range. New Phytologist. 233(4):1768-1779. https://doi.org/10.1111/nph.17904.
Li, X., Guo, T., Bai, G., Zhang, Z., See, D.R., Marshall, J., Garland Campbell, K.A., Yu, J. 2022. Genetics-inspired data-driven approaches explain and predict crop performance fluctuations attributed to changing climatic conditions. Molecular Plant. 15(2):203-206. https://doi.org/10.1016/j.molp.2022.01.001.
Wu, D., Li, X., Tanaka, R., Wood, J., Tibbs-Cortes, L., Magallanes-Lundback, M., Bornowski, N., Hamilton, J., Vaillancourt, B., Diepenbrock, C., Li, X., Deason, N., Schoenbaum, G., Yu, J., Buell, R., Dellapenna, D., Gore, M. 2022. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics. 221(4). Article iyac091. https://doi.org/10.1093/genetics/iyac091.
Li, R., Char, S., Liu, B., Liu, H., Li, X., Yang, B. 2021. High-efficiency plastome base editing in rice with TAL cytosine deaminase. Molecular Plant. 14(9):1412-1414. https://doi.org/10.1016/j.molp.2021.07.007.
