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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Research Project #434350

Research Project: Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality

Location: Wheat Health, Genetics, and Quality Research

2018 Annual Report

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.

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 project began in March of 2018 and continues research from Project Number 2090-21000-030-00D, entitled “Genetic Improvement of Wheat and Barley for Resistance to Biotic and Abiotic Stresses.” 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. Sub-objective 1A: Significant progress was made to develop and release new cultivars of club wheat. A new cultivar, ‘Castella’, was selected for purification. Castella possesses excellent grain yield, excellent end use quality for cake and cookie baking and combined seedling and adult plant resistance to stripe rust. 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 USDA-ARS breeding program supplies the raw product for a significant component of the export wheat market in the Pacific Northwest. Sub-objective 1B: Significant progress was made to select wheat breeding lines with better end-use quality and high falling numbers by combining resistance to preharvest sprouting with late maturity alpha-amylase resistance. A genome-wide association study identified the number and location of genetic loci associated with higher falling number based on data collected from field trials. The mapping panel was also assayed for resistance to preharvest sprouting using spike wetting tests under controlled conditions. Loci were identified that were specific for falling number or for preharvest sprouting or both. This research documented that preharvest sprouting was not the only cause of low falling numbers in soft white wheat. The other cause of low falling numbers, late maturity alpha amylase, also occurred. The utility of the molecular markers that were associated with falling numbers will be verified on segregating breeding populations and are already being used in regional wheat breeding programs to improve the overall resistance to low falling numbers. Sub-objective 1C: Several high-throughput field phenotyping techniques were evaluated on a segregating population of winter wheat under drought and well-watered environmental conditions in Colorado, Oregon and Washington. Progress was made in determining the best practices for data collection, ease of use, and reliability of these phenotyping methods. Use of high throughput phenotyping for indirect selection of breeding lines that are more drought or heat tolerant will continue. Better data management and analysis methods will be developed to use high throughput phenotyping as a tool for wheat breeding. Objective 2: Substantial progress was made to identify genetic resources and introgress multiple new genes for resistance to stripe rust and to soil borne diseases into wheat germplasm. Over 2000 breeding lines from public and private sector wheat breeders were evaluated at multiple locations for resistance, and data was provided for them to select stripe rust resistance in their programs. Several hundred crosses were made to incorporate genes for resistance into wheat breeding populations targeted to the major wheat production regions of the U.S. In addition, the populations of cereal cyst nematode in the Pacific Northwest were assayed and their pathogenicity was determined to be different than other previously identified populations of cyst nematodes. This research will provide breeders with the tools to breed for resistance to new pathotypes of cereal cyst nematode that are present in the western U.S. Subobjective 3B: The mechanisms controlling seed dormancy, germination, and resistance to preharvest sprouting are being identified. 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 number. These markers are being used to select this allele within the soft white winter wheat breeding program to confirm their usefulness in breeding. Alleles providing increased seed dormancy associated with altered hormone sensitivity will be combined to increase preharvest sprouting resistance. The relationship between resistance to low falling numbers due to increased dormancy and winter wheat emergence from deep sowing was investigated by scoring a large wheat population for both traits. Markers linked to emergence traits will be developed and used in conjunction with selection for improved resistance to falling number. Sub-objective 3C: Progress was made 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 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. Those populations will be evaluated over multiple years for resistance to late-maturity alpha amylase in order to determine the location and number of genetic loci for the trait. The first crosses were made between resistant and susceptible parents to develop near isogenic lines differing for specific susceptibility loci so that the effect of each locus can be determined. In addition, populations of soft and hard winter and spring wheat from regional breeding programs will be screened in collaboration with wheat breeders to improve resistance to low falling numbers due to late-maturity alpha amylase. Objective 4: The Western Small Grains Genotyping Laboratory developed a Targeted Amplicon Sequencing (TAS) approach to genotyping that provides increased numbers of data points per sequencing lane and identifies segregation for major known loci of importance to wheat breeders. The Western Regional Cooperative Nurseries 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. Molecular markers of importance to regional public and private sector breeders were assayed on these nurseries and data were reported. These services aid regional breeders to maintain the efficiency and high quality of their breeding programs so that productive wheat cultivars are available for farmers to grow.

1. Genetic loci controlling falling numbers identified (Triticum aestivum L.). Preharvest sprouting, the germination of grain before harvest, causes falling numbers below 300 seconds, which result in grain discounts, and soft white wheat is particularly susceptible. ARS researchers in Pullman, Washington, together with collaborators at Washington State University, conducted a genome-wide association study on a large adapted soft white winter wheat population over multiple years and locations under natural and induced conditions that triggered low falling numbers. Genetic loci were identified for resistance to preharvest sprouting and for falling number per se, but these loci were not always the same for both traits, indicating that other factors also contributed to low falling numbers in soft white winter wheat. Regional wheat breeders are using the molecular markers that were identified to select for resistance in their own breeding programs so that producers can reduce their risk of discounts resulting from low falling numbers caused by preharvest sprouting.

2. Ability of winter wheat (Triticum aestivum L) to tolerate freezing. Measured freezing tolerance of winter wheat plants has long been known to be inexplicably, highly variable. ARS researchers in Pullman, Washington, discovered that young winter wheat plants, grown under 12-hour light/12 hour darkness at constant low temperature (4 degrees Centigrade) varied dramatically in their ability to tolerate exposure to subfreezing temperatures, depending on the time of day. Nearly 20 percent greater survival was found if the plants were exposed to subfreezing temperatures in the middle of the dark period, or the middle of the light period, compared to exposure starting at the end of either period, and freezing tolerance cycled from low to high twice in each 24-hour period. Expression analyses of cold-responsive genes and metabolite concentrations showed that most cycled from low to high once per day, leading to the conclusion that at least two distinct signaling pathways, one conditioning freezing tolerance in the light, and one conditioning freezing tolerance in the dark, are active in the wheat plants. The influence of the time of day must be considered for artificial freezing trials to accurately predict freezing survival for winter wheat in the field.

3. Loss of seed dormancy in dry seeds. Preharvest sprouting, the initiation of germination on the mother plant, is one major cause of low falling numbers, which result in poor flour functionality, due to the presence of the enzyme alpha-amylase in the grain. Resistance to preharvest sprouting in wheat (Triticum aestivum L) results largely from seed dormancy, the inability to germinate under favorable conditions. When ARS researchers in Pullman, Washington, used the model plant, Arabidopsis, to compare the transcriptomes of dry after-ripened highly dormant seeds possessing the sly1 mutation with Arabidopsis seeds without the mutation, dormancy loss through after-ripening was associated with increased expression of protein translation genes and decreased expression of histone deacetylase, an enzyme that inhibits gene transcription. The prevention of seed germination in seed dormancy occurs through control of fundamental cellular processes, illustrating that this critical survival trait is essential to seed biology.

4. Near-infrared spectrometry (NIR) as a rapid proxy for the falling number test. Addition of small amounts of low falling number wheat to high falling number wheat results in unacceptable product because the enzyme alpha-amylase is effective at low concentrations. Farmers and elevators must currently wait two weeks for results from the commercial falling numbers test, and, consequently, low falling number wheat is inadvertently mixed with high falling number wheat, resulting in unacceptable financial losses to growers and grain elevators. ARS scientists in Pullman, Washington, and Beltsville, Maryland, collaborated to determine if near-infrared spectrometry (NIR) could be used to rapidly sort high and low falling number grain. While it was possible to find a calibration that worked in one environment, it was not possible to arrive at a calibration that would work for all environments. This is likely because low falling number is caused by two phenomena, preharvest sprouting and late maturity alpha amylase. Published papers claiming that NIR can replace falling number tests are incorrect.

Review Publications
Delwiche, S.R., Steber, C.M. 2018. Falling number of soft wheat wheat by near-infrared spectroscopy: a challenge revisited. Cereal Chemistry. 95(3):469-477.
Martinez, S.A., Thompson, A.L., Wen, N., Murphy, L.R., Sanguinet, K., Steber, C.M., Garland Campbell, K.A. 2018. Registration of the LouAlp (Louise/Alpowa) wheat recombinant inbred line mapping population. Journal of Plant Registrations. https://doi:10.3198/jpr2017.08.0053crmp.
Skinner, D.Z., Bellinger, B.S., Hiscox, W., Helms, G. 2018. Evidence of cyclical light/dark-regulated expression of freezing tolerance in young winter wheat plants. PLoS ONE. 13(6).
Liu, L., Wang, M., Feng, J., See, D.R., Chao, S., Chen, X. 2018. Combination of all-stage and high-temperature adult-plant resistance QTL confers high level, durable resistance to stripe rust in winter wheat cultivar Madsen. Theoretical and Applied Genetics. https://doi 10.1007/s00122-018-3116-4.
Gizaw, S.A., Godoy, J.V., Garland Campbell, K.A., Carter, A.H. 2018. Using spectral reflectance indices as proxy phenotypes for genome-wide association studies of yield and yield stability in Pacific Northwest winter wheat. Crop Science. https://doi:10.2135/cropsci2017.11.0710.
Lewein, M.J., Murray, T.D., Jernigan, K.L., Garland Campbell, K.A., Carter, A.H. 2018. Genome-wide association mapping for eyespot disease in US Pacific Northwest winter wheat. PLoS One.
Zhang, C., Si, Y., Lamkey, R., Boydston, R.A., Garland Campbell, K.A., Sankaran, S. 2018. High-throughput phenotyping of seed/seedling evaluation using digital image analysis. Agronomy.
Jernigan, K.L., Godoy, J.G., Huang, M., Zhou, Y., Morris, C.F., Garland Campbell, K.A., Zhang, Z., Carter, A.H. 2018. Genetic dissection of end-use quality traits in adapted soft white winter wheat. Frontiers in Plant Science.