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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Research Project #424575

Research Project: Genetic Improvement of Wheat and Barley for Resistance to Biotic and Abiotic Stresses

Location: Wheat Health, Genetics, and Quality Research

2018 Annual Report

Objective 1. Identify and develop wheat germplasm adapted to the Pacific Northwest of the United States with improved tolerance to pre-harvest sprouting, drought stress, cold temperatures, rusts, and soil-borne diseases. 1A. Identify sources of drought, cold, and disease tolerance by phenotyping subsets of the National Small Grains Collection as well as international and regional nurseries. 1B. Reduce production risk by developing germplasm with increased resistance to stripe and stem rust. 1C. Breeding club wheat and hard white winter wheat. Objective 2: Develop more efficient wheat and barley breeding approaches based on high throughput phenotyping and genotyping methods as well as genomic selection models. 2A. Identify and apply SNP markers for basic biology and MAS in wheat and barley. 2B. Develop high-throughput phenotyping methods for measuring freezing and drought tolerance. 2C. Develop statistical models for genotype response to environmental stress that improve the efficiency of selection and breeding. Objective 3: Investigate the mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat. 3A. Identify and combine physiological mechanisms that support yield under water stress in wheat including water-use efficiency, root architecture, and photosynthetic efficiency. 3B. Transcriptome analysis of post cold-acclimation stress response. 3C. Gene Expression profiling and biochemical pathway discovery for stripe rust resistance. 3D. Examine the role of the plant hormones ABA and GA in controlling seed dormancy, germination, and preharvest sprouting tolerance.

Objective 1. We will evaluate a total of 6,356 accessions for resistance to freezing injury, Fusarium crown rot, lesion nematodes, cyst nematodes, and stripe rust. We will conduct these evaluations using facilities at WSU, including controlled environments in the WSU Plant growth facility and at the Spillman Agronomy Farm. We will use the genomic information generated by the T-CAP for the existing core collection to link phenotypes to genotypes. We will also screen germplasm from U.S. regional nurseries. These selections will be genotyped to determine relationships and, on the theory that genetic control of resistance will be different among genetically diverse genotypes, traits from the most diverse will be introgressed into adapted cultivars, and germplasm adapted to various regions of the U.S. carrying unique new sources of resistance and molecular markers that can be used to select for these new resistance loci. Objective 2. Specific areas that are being targeted in SNP development include identification of SNP markers linked to stem and stripe rust resistance genes, climatic resilience and identification of SNP in wheat responsible for regional and market class adaptation. The current small grains single plant core collections are being evaluated for SNP linkages to drought, stripe, leaf and stem rust response. As new, verified markers are identified, they will be made available to the customers of the genotyping laboratory as applicable to the customers’ research and breeding objectives. Our goal is to transition away from single gene selection using SSR markers, genotyping by sequencing and incorporate genome selection utilizing SNPs through SNP-chip platforms. Objective 3. Pathways and mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat will be elucidated. Indirect selection for tolerance to freezing and to drought based on physiological traits associated with drought and freezing tolerance will be carried out as part of the selection process. Plant lines will be selected for higher water use efficiency, deeper roots, and higher photosynthetic efficiency to develop better grain yield and grain-filling under drought stress. Transcriptome analysis will be used to identify pathways and mechanisms responding to freezing stress and stripe rust. Key genes will be identified and their expression monitored under stress conditions, thereby identifying plant lines differing in their abilities to respond to parts of the freezing or infection process. Variation in sensitivity to plant hormones will be investigated as a means to control and improve seedling emergence and preharvest sprouting tolerance. These different abilities and sensitivities will be genetically combined, resulting in improved stress tolerance.

Progress Report
This is the final report for this project which terminated in March 2018. Substantial results were realized over the five years of the project. Progress was made on all three objectives and sub-objectives, which fall under National Program 301, Component I, Crop Genetic Improvement; Component 2, Crop Genetic and Genomic Resources and Information Management, and Component 3, Crop Biological and Molecular Processes. The new project 2090-21000-033-00D, "Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality", continues several aspects of this research. Sub-objective 1A: Significant progress was made in discovering and validating new genetic markers associated with winter survival and resistance to the soil borne diseases snow mold and Fusarium crown rot, which severely impact winter survival. The genetic control of resistance to stripe rust (also known as yellow rust) (Puccinia striiformis) was identified in new landrace sources of resistance and molecular markers associated with that resistance were developed so that it could easily be combined with existing resistance genes for more durable control. Under Sub-objective 1B, 1209 genotypes were evaluated for resistance to cereal cyst nematode (Heterodera species) in replicated field trials over the five-year period and 207 genotypes with lower nematode counts were determined to be resistant to either H. filipjevi or H. avenae. Further screening and confirmation of resistance is being conducted as part of the replacement project, 2090-21000-033-00D. This was the first documentation of resistance to cereal cyst nematode in wheat adapted to the United States. Resistance to stripe rust was evaluated in 1370 advanced breeding lines in uniform nurseries and 6907 early generation breeding lines from U.S. public and private sector wheat breeders in field and greenhouse seedling screening environments. All of this data was reported back to individual breeding programs and used by them to select for resistance to this disease, which is the primary cause of wheat yield losses worldwide. Stripe rust resistance was introgressed from the germplasm that has been developed in the USDA-ARS wheat breeding program at Pullman into advanced breeding lines suggested by other wheat breeders. After four years, 1,279 populations from crosses between resistant germplasm and advanced breeding lines were developed. The initial set of these ‘shuttle breeding’ populations were selected for resistance in the field in 2017. The resistant selections were harvested and returned to breeders, so they can begin to work with them during the 2018 cropping season. A prebreeding program for stripe rust resistance was initiated, working with more exotic and novel sources of stripe rust resistance, combined with male sterility to facilitate crossing, and backcrossed to adapted soft and hard wheat cultivars. This prebreeding effort will continue as part of the replacement project. Sub-objective 1C: Plots and head rows were evaluated in 12 locations and in controlled growth facilities to develop improved cultivars of club wheat, a specialty class of soft white wheat that is only grown in the Pacific Northwest. Early generation breeding lines were evaluated for resistance to stripe rust, soil borne disease, emergence and adaptation for early maturity in nurseries at five locations. Cultivars and breeding lines were released to continue to offer growers several excellent options for the club wheat market class. ‘ARS Crescent’, was released in 2012 and was the leading club wheat cultivar in 2017. It was planted on 98,484 acres due to its resistance to preharvest sprouting as compared to the previous predominant cultivar ‘Bruehl’. The club wheat cultivar ‘Pritchett’, was released in 2015 and is currently being increased as registered seed, available to growers in the fall of 2018. There is strong demand. The breeding line, ARS20060123-31C was named ‘Castella’, with excellent stripe rust resistance, tolerance to high aluminum in soils, tolerance to low falling numbers, excellent soft wheat quality and yield potential and moderately early maturity. Castella was purified in 2017 and will be increased for release in 2018 as part of the replacement project. Sub-objective 2A: More than 27.6 million genotyping by sequencing DNA marker tags, along with agronomic and disease resistance data were provided to wheat and barley breeders in the western U.S. A database of sequence variants was developed and is being used to conduct targeted amplicon sequencing (TAS) under the replacement project. The TAS technology provides breeding programs with a large number of molecular markers linked to important selection targets, greatly facilitating selection and plant improvement efforts. Sub-objective 2B: A method of reproducibly testing 96 plant accessions simultaneously for freezing tolerance was developed. Sub-objective 2C: Computer scripts were developed and used to analyze next-generation sequencing data for several bi-parental studies and association mapping trials. The scripts provide pre-processing functions to filter out tags of unacceptable occurrence frequencies and those likely to have sequencing errors. These scripts have provided genotype data for genome wide association studies (GWAS) and for genomic selection. Mixed model analysis was used to develop spatial models for analysis of variety trial data. Correcting for major trends and smaller scale spatial variation improved the predictions in every case over standard randomized complete block and even over alpha-lattice designs. These new methods of analyses resulted in better predictions of varietal and breeding line performance. Sub-objective 3A: Two large adapted wheat populations were evaluated for preharvest sprouting, alpha amylase, and falling number using grain grown at two locations over multiple years. Spike wetting tests, which mimic natural conditions causing preharvest sprouting, were also conducted at the Washington State University (WSU) plant growth facility. Since 2012, 11,509 datapoints were generated for falling number from the multiple locations in the Washington statewide extension trials. Data were provided to farmers and the grain industry in a web-accessed database ( This large database of accurate falling numbers data was used by farmers to select wheat cultivars for planting and it is the basis of ongoing research as part of the replacement project to identify the effect of the cultivar and the environment on the risk of low falling numbers. Sub-objective 3B: The freezing tolerance of wheat plants was discovered to be based on multiple complex systems characterized by sequential cascades of gene expression, dependent on interactions of time, photoperiod, and temperature (both above and below freezing). Different wheat lines may use different mechanisms as their predominant means of response to low temperature. Breeding approaches to combine these response mechanisms are continuing under the replacement project. Sub-objective 3C: Gene expression profiling and biochemical pathway discovery for stripe rust resistance were conducted. The purpose of this research is to move beyond just identifying genetic markers and to discern the causes and relationships among resistance mechanisms. Sub-objective 3D: The hormonal control of preharvest sprouting in wheat was investigated. Sprout tolerance results from seed dormancy, the inability to germinate until grain has been stored dry for a while (after-ripened) which is regulated by the plant hormones gibberellin and abscisic acid. The Enhanced Response to abscisic acid (ABA) hormone 8 (ERA8) gene was mapped and molecular markers were identified that are being used to cross this locus into adapted winter and spring breeding lines under the replacement project. Please see the annual report for the new or replacement project, 2090-21000-033-00D, "Genetic Improvement of Wheat and Barley for Environmental Resilience, Disease Resistance, and End-use Quality", for further information.

1. Pritchett club wheat increased and is available for farmer purchase. The current major club wheat cultivar Bruehl is susceptible to poor quality due to low falling numbers, and the other major club wheat cultivar ARS Crescent has only moderate resistance to current races of stripe rust. The USDA-ARS wheat breeding program at Pullman, Washington, in collaboration with colleagues at Washington State University, selected and released Pritchett club wheat from a cross between the older club wheat cultivars Bruehl and Chukar. Pritchett has been increased as breeder and foundation seed through the Washington State Crop Improvement Association and combines the good emergence and stripe rust resistance of Bruehl with the excellent grain quality of Chukar. The availability of this new club wheat cultivar for farmers to purchase in fall of 2018 will further enhance the global wheat trade and specifically the soft white wheat export market from the Pacific Northwest to Japan and other Asian countries.

2. Isolation of non-GMO glyphosate tolerant wheat. Genetically modified or transformed wheat is considered unacceptable by consumers. ARS scientists in Pullman, Washington, in collaboration with Washington State University scientists, identified and characterized glyphosate resistant mutants in wheat. While these mutants were not sufficiently resistant to yield well after treatment with glyphosate at modern application rates, the research proves that it is feasible to obtain resistance without a genetic transformation event. These results corroborated research from other laboratories on the mechanisms of resistance to glyphosate in plants and strengthen the need for new research to identify alternatives to glyphosate in cropping systems.

Review Publications
Nelson, S.K., Ariizumi, T., Steber, C.M. 2017. Biology in the dry seed: transcriptome changes associated with Arabidopsis seed dormancy and dormancy loss in the GA-insensitive sleepy1 mutant. Frontiers in Plant Science.
Martinez, S.A., Tuttle, K.M., Takebayashi, Y., Seo, M., Garland Campbell, K.A., Steber, C.M. 2016. The wheat ABA hypersensitive ERA8 mutant is associated with increased preharvest sprouting tolerance and altered hormone accumulation. Euphytica. 212(2):229-245.
Aramrak, A., Lawrence, N.C., Demacon, V.L., Carter, A.H., Kidwell, K.K., Burke, I.C., Steber, C.M. 2018. Mutations conferring increased glyphosate resistance in spring wheat, Triticum aestivum (L.). Crop Science. 58:84-97.
Martinez, S.A., Godoy, J., Huang, M., Zhang, Z., Carter, A.H., Garland Campbell, K.A., Steber, C.M. 2018. Genome-wide association mapping for tolerance to preharvest sprouting and low falling numbers in wheat. Frontiers in Plant Science. 9:141.
Boehm, J.D., Ibba, M., Kiszonas, A., See, D.R., Skinner, D.Z., Morris, C.F. 2018. Genetic analysis of kernel texture (grain hardness) in a hard red spring wheat (Triticum aestivum L.) bi-parental population. Journal of Cereal Science. 79:57-65.
Boehm, J.D., Ibba, M., Kiszonas, A., See, D.R., Skinner, D.Z., Morris, C.F. 2017. Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.). Journal of Cereal Science. 77:73-83.
Skinner, D.Z. 2017. Advances in cold-resistant wheat varieties. In Langridge, P., editor. Achieving Sustainable Cultivation of Wheat. Volume 1. Cambridge, UK:Burleigh Dodds Science Publishing. p. 153-173.
Mahoney, A.K., Babiker, E.M., See, D.R., Paulitz, T.C., Okubara, P.A., Hulbert, S.H. 2017. Analysis and mapping of Rhizoctonia root rot resistance traits from the synthetic wheat (Triticum aestivum L.) line SYN-172. Molecular Breeding. https://doi 10.1007/s11032-017-0730-9.
Lu, Y., Wang, M., Chen, X., See, D.R., Chao, S., Jing, J. 2014. Mapping of Yr62 and a small effect QTL for high-temperature adult-plant resistance to stripe rust in spring wheat PI 192252. Theoretical and Applied Genetics. 127:1449-1459.
Mahoney, A., Babiker, E.M., Paulitz, T.C., See, D.R., Okubara, P.A., Hulbert, S. 2016. Characterizing and mapping resistance in synthetic-derived wheat to Rhizoctonia root rot in a green bridge environment. Phytopathology. 106:1170-1176.
Mahoney, A., Babiker, E.M., Okubara, P.A., See, D.R., Paulitz, T.C., Hulbert, S.H. 2017. Analysis and mapping of Rhizoctonia root rot resistance traits from the synthetic wheat (Triticum aestivum L.) line SYN-172. Molecular Breeding. 37:130.
Cook, J.P., Heo, H., Varella, A.C., Lanning, A.C., Blake, N.K., Sherman, J.D., Martin, J.M., See, D.R., Chao, S., Talbert, L.E. 2018. Evaluation of a QTL mapping population composed of hard red spring and winter wheat alleles using various marker platforms. Crop Science. 58:701-712.
Wang, R., Chen, J., Anderson, J.A., Zhang, J., Zhao, W., Wheeler, J., Klassen, N., See, D.R., Dong, Y. 2017. Genome-wide association mapping of fusarium head blight resistance in spring wheat lines developed in Pacific Northwest and CIMMYT. Phytopathology. 107(12):1486-1495.
Manning-Thompson, Y., Thompson, A., Paulitz, T.C., Smiley, R., Garland Campbell, K.A. 2016. Cereal cyst nematode screening in locally adapted spring wheat (Triticum aestivum L.) germplasm of the Pacific Northwest, 2015. Plant Disease Management Reports. 10:N003.
Jernigan, K.L., Morris, C.F., Zemetra, R., Chen, J., Garland Campbell, K.A., Carter, A.H. 2017. Genetic analysis of soft white wheat end-use quality traits in a club by common wheat cross. Journal of Cereal Science. 76:148-156.
Liu, W., Naruoka, Y., Miller, K., Garland Campbell, K.A., Carter, A.H. 2018. Characterizing and validating stripe rust resistance loci in US Pacific Northwest winter wheat accessions (Triticum aestivum L.) by genome-wide association and linkage mapping. The Plant Genome.
Case, A., Naruoka, Y., Chen, X., Garland Campbell, K.A., Zemetra, R.S., Carter, A.H. 2014. Mapping stripe rust resistance genes in a Brundage x Coda winter wheat recombinant inbred line population. PLoS One. 9(3):e91758.