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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

2014 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: Multiple samples from the National Small Grains Collection (NSGC) core collection have been evaluated for novel QTL for both abiotic and biotic stresses. A group of spring wheats from the NSGC were evaluated for resistance to stem and stripe rust. A molecular phylogeny was developed identifying landraces that have stem rust resistance, stripe rust resistance and lines with resistance to both types of rusts. This manuscript was published in Crop Science 2014 DOI: 10.2135, “Genetic diversity for stripe rust resistance in wheat landraces and identification of accessions with resistance to stem rust and stripe rust”. Association mapping and lab experiments were performed on a group of winter wheat landraces from the NSGC. Both bioinformatics and freezing tolerance assays confirmed that increased freezing tolerance was observed in landraces which were collected from locations above 40 degrees latitude. Minicore subsets of the NSGC core collection for wheat have been identified and the first part of these have been screened for resistance to cold and to fusarium. Regional nurseries have been evaluated for resistance to stripe rust, cyst nematode, cold tolerance and fusarium. Club, soft wheat and hard wheat germplasm with resistance to stripe rust have been developed and distributed to other breeders via the regional nursery system. A cooperative crossing and evaluation program was initiated to introgress stripe rust resistance into U.S. wheat germplasm. Club wheat breeding lines with resistance to multiple diseases, excellent quality and competitive production characteristics were entered into state extension trials for final evaluation prior to release. 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. Genotype by Sequence (GBS) technology has been acquired, GBS methodology is being optimized and bioinformatics pipelines have been developed to select sequence tags for genomic selection modeling. B. Carbon isotope discrimination and canopy temperature measurement were characterized as selection methods to screen wheat for increased water use efficiency and rooting depth, respectively, in the Louise/Alpowa RIL populations. C. Seed from over 3500 lines selected from an eight-parent diallel cross were produced in the field. These lines are undergoing freezing tolerance evaluations in controlled environment chambers. Replicated tests at three target temperatures are underway. Objective 3: Investigate the mechanisms controlling drought and cold tolerance, pre-harvest sprouting, and rust resistance in wheat. A. A linkage map was developed for the Louise/Alpowa RIL population using 9000 SNP chip genotyping data. QTL analysis of the Louise/Alpowa population for Water Use Efficiency, canopy temperature, photosynthetic yield (Phi-PS2), and for yield is in process. B. Transcriptome analysis using microarrays has been completed for multiple time points of an investigation of freeze-thaw enhanced freezing tolerance. About 50 genes appear to be key to the freezing tolerance enhancement effect and are being investigated further. C. A group of spring wheats from the NSGC was evaluated for resistance to stem and stripe rust. A molecular phylogeny was developed identifying landraces that have stem rust resistance, stripe rust resistance and lines with resistance to both types of rusts. This manuscript was published in Crop Science 2014 doi:10.2135, “Genetic diversity for stripe rust resistance in wheat landraces and identification of accessions with resistance to stem rust and stripe rust”. D. Preharvest sprouting (PHS) tolerance was found to be associated with high abscisic acid (ABA) hormone sensitivity and low gibberellic acid (GA) hormone sensitivity. As PHS tolerant cultivars lost seed dormancy through dry after-ripening (a period of dry storage) and cold imbibing (wet chilling) they first showed increasing germination in response GA, and late with increasing insensitivity to ABA’s inhibition of seed germination. In the model Arabidopsis, data suggests that increasing GA sensitivity with seed dormancy loss may be due to increased expression of the GA hormone receptor GID1.


Accomplishments
1. Preharvest sprouting tolerance in northwest wheat cultivars. Northwest farmers suffered devastating losses as a result of rain-triggered sprouting of the young seeds on the plants before they could be harvested in 2011 and 2013. Sprouted grain damages the starch when wheat flour is made into dough, making the flour unacceptable for customary products for human consumption. ARS researchers in Pullman, Washington, with Washington State University collaborators, characterized cultivars and breeding lines from the Pacific Northwest for their ability to tolerate wet conditions without sprouting, and analyzed sprout damage in wheat harvested from 20 locations in 2013. Large variation in preharvest sprouting tolerance was found and discussed at three grower’s conferences, posted on the web, and published in the grower’s magazine, “Wheat Life". This information will help farmers to choose existing varieties with better preharvest sprouting tolerance for planting, and will assist wheat breeders in developing cultivars with superior preharvest sprouting tolerance.

2. Genes for improved frost tolerance. It is known that variation in the ability of winter wheat to survive the winter months in the field is associated with differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) genes, but knowledge of specific allelic influence and possible interactions among these genes is lacking. ARS researchers in Pullman, Washington, assayed variation in the composition and the number of copies of the genes at the FR2 and VRN1 loci in a large set of winter and spring wheat genotypes from around the world representing a broad range of freezing tolerance. The results suggest that selection of varieties carrying a specific form of the FR2 gene (the FR-A2-T allele) and three copies of the recessive vrn-A1 allele would be a good strategy to improve frost tolerance in winter wheat. These findings provide wheat breeders with new molecular tools to select for winter survival in wheat.

3. Hormone and sensitivity in wheat and Arabidopsis seeds. The problem is that seed dormancy provides preharvest sprouting tolerance in wheat, but much remains to be learned about the hormonal control of seed dormancy and seed dormancy loss. Preharvest sprouting tolerance was associated both with high sensitivity to the dormancy-inducing hormone abscisic acid (ABA) and with low sensitivity to the germination-promoting hormone gibberellic acid (GA). Hormone profiling showed that seed dormancy was associated with elevated internal levels of ABA hormone both in wheat and in the model system Arabidopsis. As seed dormancy was lost, ABA levels decreased and GA levels increased. In wheat seed dormancy loss was also associated with changes in the plant hormone jasmonic acid (JA), suggesting that this hormone may also play a role in regulating seed dormancy loss. In providing foundational knowledge about the hormonal control of seed dormancy, this research will assist in the development of preharvest sprouting tolerant wheat cultivars.

4. The role of lipids in increasing wheat freezing tolerance. How the processes involved in freezing tolerance and winterhardiness of winter wheat are initiated and propagated throughout the plant is unknown. ARS researchers in Pullman, Washington, have identified specific sets of plant lipids that rapidly increase in concentration in response to cold temperature and reach high concentration in plants that have developed good freezing tolerance. These lipids resulted in increased freezing tolerance when extracted and applied to young seedlings, suggesting the lipids play a key role in the initiation and propagation of signals involved in cold temperature stress response. This research will lead to fundamental new knowledge of the processes wheat plants use to develop and sustain freezing tolerance and survive the winter months, and thereby provide a means of developing more winterhardy wheat cultivars.


Review Publications
Martinez, S., Schramm, E.C., Harris, T.J., Kidwell, K.K., Garland Campbell, K.A., Steber, C.M. 2014. Registration of Zak ERA8 soft white spring wheat germplasm with enhanced response to ABA and increased seed dormancy. Journal of Plant Registrations. 8(2)217-220. DOI: 10.3198/jpr2013.09.0060crg.
Skinner, D.Z. 2014. Time and temperature interactions in freezing tolerance of winter wheat. Crop Science. 54:1-7. DOI: 10.2135/cropsci2013.09.0623.
Skinner, D.Z., Garland Campbell, K.A. 2014. Measuring freezing tolerance: Survival and regrowth assays. In:Hincha, D.K., Zuther, E., editors. Plant Cold Acclimation. United Kingdom:Humana Press. p. 7-13.
Skinner, D.Z., Bellinger, B.S., Hansen, J.C., Kennedy, A.C. 2014. Carbohydrate and lipid dynamics in wheat crown tissue in response to mild freeze-thaw treatments. Crop Science. 54:1–8. DOI: 10.2135/cropsci2013.09.0604.
Zhu, J., Pearce, S., Burke, A., See, D.R., Skinner, D.Z., Dubcovsky, J., Garland Campbell, K.A. 2014. Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theoretical and Applied Genetics. 127(5):1183-1197.
Skinner, D.Z. 2014. Real-time PCR: Advanced technologies and applications. Crop Science. 24:1:455-456.
Smiley, R., Marshall, J.M., Gourlie, J.A., Paulitz, T.C., Kandel, S.L., Pumphrey, M.O., Garland Campbell, K.A., Yan, G., Anderson, M.D., Flowers, M.D., Jackson, C.A. 2013. Spring wheat tolerance and resistance to Heterodera avenae in the Pacific Northwest. Plant Disease. 97(5):590-600.
Kandel, S.L., Smiley, R.W., Garland Campbell, K.A., Elling, A.A., Abatzoglou, J., Huggins, D.R., Rupp, R., Paulitz, T.C. 2013. Relationship between climatic factors and distribution of Pratylenchus spp. in the dryland wheat production areas of Eastern Washington. Plant Disease. 97:1448-1456.
Case, A.J., Skinner, D.Z., Garland Campbell, K.A., Carter, A.H. 2014. Freezing tolerance-associated QTL in the Brundage × Coda wheat recombinant inbred line population. Crop Science. 54:982-992. DOI: 10.2135/cropsci2013.08.0526.
Sthapit, J., Newcomb, M.S., Bonman, J.M., Chen, X., See, D.R. 2014. Genetic diversity for stripe rust Resistance in wheat landraces and identification of accessions with resistance to stem rust and stripe rust. Crop Science. doi: 10.2135/cropsci2013.07.0438.
Hauvermale, A., Ariizumi, T., Steber, C.M. 2014. The roles of the GA receptors GID1a, GID1b, and GID1c in sly1-independent GA signaling. Plant Signaling and Behavior. 9:e28030; PMID: 24521922.