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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

2015 Annual Report


Objectives
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.


Approach
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
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. In 2015, we made 181 crosses for improved agronomic and quality traits and to combine resistance to stripe rust and multiple soil borne diseases into germplasm adapted to the Pacific Northwest. We made 167 crosses to introgress stripe rust resistance into germplasm adapted to the Great Plains and the Eastern and Southern U.S. and developed breeding lines with an average of nine loci for rust resistance combining seedling and adult plant resistance. We evaluated 4600 plots and 30,960 head rows and entered nine advanced breeding lines into regional and extension trials. Two of these lines will be proposed for increase as cultivars and up to six are on increase for release as germplasm. A complex population was developed with resistance to lesion nematodes and to Fusarium crown rot and is being evaluated for lignin content and resistance to additional diseases; this population has been released for worldwide public access. Objective 2: Develop more efficient wheat and barley breeding approaches based on high throughput phenotyping and genotyping methods as well as genomic selection models. A. Multiple bi-parental mapping populations were evaluated using sequence tags. A database of mapped sequence tags is being compiled to develop a comprehensive annotation file for imputing (filling in missing data) for the purpose of association mapping and genetic populations. B. Develop high-throughput phenotyping methods for measuring freezing and drought tolerance. We evaluated the Winter Wheat Core nursery (1600 lines) for resistance to freezing and increased root health by evaluating the spring wheat core nursery for resistance to Fusarium crown rot. Freezing tolerance in winter wheat based on our screening method was highly correlated to field survival. C. Computer scripts were written to analyze next-generation sequencing data, resulting in mapped DNA sequence tags for bi-parental studies and frequency tallies of DNA tags in association panels. The scripts provide pre-processing functions to filter out tags of unacceptable occurrence frequencies and those likely to have sequencing errors. Objective 3: Investigate the mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat. A. Agronomic and physiological traits were measured in a spring wheat population over 12 environments with 14.5 to 50cm annual precipitation. Plant growth and kernel traits were correlated with grain yield but physiological traits were not. Plant morphology and kernel traits can augment indirect selection for drought resistance in early generations. B. Transcriptome analysis revealed that fully-acclimated winter wheat activates numerous physiological mechanisms in response to temperatures low enough to initiate ice formation within the plant. These responses diversify with time in both the numbers of genes responding and the breadth of physiological processes involved, indicating a complex, multi-faceted response. C. Four mapping populations developed from Sthapit et al. 2014 were genotyped. QTL for seedling resistance to stripe rust were identified in all populations. Three populations had major QTL responsible for resistance and are excellent candidates for introgression into adapted germplasm to increase levels of resistance. D. Wheat recombinant inbred lines were planted under dry conditions to screen for higher drought tolerance under dry conditions. Wheat was screened for degree of preharvest sprouting tolerance based on the Hagberg Falling Number tests, the spike wetting test, and alpha-amylase analysis. Wheat cultivars were also screened for susceptibility to another cause of low falling number, Late Maturity alpha-amylase (LMA). This research revealed that there is some susceptibility for LMA in northwest germplasm. This research will help wheat breeders to select for preharvest sprouting and LMA resistance in breeding lines. This will protect farmers from financial loss due to discounts as a result of low falling numbers due either to sprouting or LMA.


Accomplishments
1. Complex responses of winter wheat to subzero temperatures. Improvement of freezing tolerance through conventional breeding approaches has been problematic and has met little success. ARS scientists at Pullman, Washington, investigated the gene expression changes that occur when plants are exposed to temperatures low enough to initiate ice formation within the plant. Numerous metabolic processes were activated, and these responses diversified with time, indicating that there are multiple points where the freezing tolerance response can fail. Based on this discovery, molecular tools are being developed to identify plant lines that effectively activate different parts of the freezing stress response, enabling breeders to genetically combine these functions into plant lines with superior freezing tolerance and winterhardiness.

2. Wheat preharvest sprouting tolerance and higher seed dormancy are associated with differences in hormone sensitivity. Germination of grain on the mother plant when cool rainy conditions occur before harvest drastically reduces the quality and utility of the grain. ARS researchers in Pullman, Washington, found that reduced sprouting was associated with sensitivity to the hormone abscisic acid and lower sensitivity to the hormone gibberellic acid during seed germination. This discovery led to the development of a laboratory assay to provide consistent selection for preharvest sprouting tolerance. This new selection tool can be used by breeders to develop wheat lines with reduced tendency to sprout on the plant, contributing to new, high quality cultivars.


Review Publications
Cuevas, C., Bellinger, B.S., Skinner, D.Z. 2014. Membrane stability of winter wheat plants exposed to subzero temperatures for variable lengths of time. Communications in Plant Sciences. 5(1-2):9-14.
Baek, K.H., Skinner, D.Z. 2012. Production of reactive oxygen species by freezing stress and the protective roles of antioxidant enzymes in plants. Journal of Agricultural Chemistry. 1:34-40.
Zurn, J.D., Newcomb, M.S., Rouse, M.N., Jin, Y., Shiaoman, C., Sthapit, J., See, D.R., Wanyera, R., Njau, P., Bonman, J.M., Brueggeman, R., Acevedo, M. 2014. High density mapping of a resistance gene to Ug99 from an Iranian landrace. Molecular Breeding. 34:871-881.
Cheng, P., Xu, L., Wang, M., See, D.R., Chen, X. 2014. Molecular mapping of genes Yr64 and Yr65 for stripe rust resistance in hexaploid derivatives of durum wheat accessions PI 331260 and PI 480016. Theoretical and Applied Genetics. 127:2267–2277.
Hauvermale, A.L., Tuttle, K.M., Takebayashi, Y., Mitsunori, S., Steber, C.M. 2015. Loss of Arabidopsis thaliana seed dormancy is associated with increased accumulation of the GID1 GA hormone receptors. Plant Cell Physiology. 56(9):1773-1785.
Naruoka, Y., Garland Campbell, K.A., Carter, A. 2015. Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.). Field Crops Research. doi: 10.1007/s00122-015-2492-2.
Skinner, D.Z. 2015. Genes upregulated in winter wheat (Triticum aestivum L) during mild freezing and subsequent thawing suggest sequential activation of multiple response mechanisms. PLoS One. 10(7):e0133166.
Tuttle, K.M., Martinez, S., Schramm, E.C., Takebayashi, Y., Seo, M., Steber, C.M. 2015. Grain dormancy loss is associated with changes in ABA and GA sensitivity and hormone accumulation in bread wheat, Triticum aestivum (L.). Seed Science Research. 25(2):179-193.
Bonman, J.M., Babiker, E.M., Cuesta-Marcos, A., Esvelt Klos, K.L., Brown Guedira, G.L., Chao, S., See, D.R., Chen, J., Akhunov, E., Zhang, J., Bockelman, H.E., Gordon, T.C. 2015. Genetic diversity among wheat accessions from the USDA National Small Grains Collection. Crop Science. 55(3):1243-1253.
Hou, L., Chen, X., Wang, M., See, D.R., Chao, S., Bulli, P., Jing, J. 2015. Mapping a large number of QTL for durable resistance to stripe rust in winter wheat Druchamp using SSR and SNP markers. PLoS One. 10(5):e0126794.
Guy, S.O., Wysocki, D.J., Schillinger, W.F., Chastain, T.G., Karow, R.S., Garland Campbell, K.A., Burke, I.C. 2013. Camelina: Adaptation and performance of genotypes. Field Crops Research. 155:224-232.
Thompson, A.L., Smiley, R.W., Garland Campbell, K.A. 2015. Registration of the LouAu (Louise/IWA8608077) wheat recombinant inbred line mapping population. Journal of Plant Registrations. doi: 10.3198/jpr2015.01.0002crmp.