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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Research Project #424855

Research Project: Genetic Improvement of Hard Winter Wheat to Biotic and Abiotic Stresses

Location: Hard Winter Wheat Genetics Research

2016 Annual Report

Objective 1: Identify and develop adapted hard winter wheat germplasm with improved resistance to leaf rust, stripe rust, stem rust, Hessian fly, Fusarium head blight, and with tolerance to heat and drought stress. Sub-objective 1.A: Develop germplasm with resistance to leaf rust, yellow rust, and stem rust. Sub-objective 1.B: Develop germplasm with resistance to Hessian fly. Sub-objective 1.C: Develop germplasm with resistance to Fusarium head blight. Sub-objective 1.D: Develop germplasm with tolerance to post-anthesis heat stress. Sub-objective 1.E: Develop germplasm with tolerance to drought stress. Sub-objective 1.F: Conduct cooperative development of hard winter wheat cultivars. Objective 2: Develop more efficient wheat breeding techniques based on high-throughput phenotyping and genotyping methods as well as genomic selection models. Sub-objective 2.A: Develop new high-throughput phenotyping platform for rapid assessment of agronomic and physiological traits in field trials. Sub-objective 2.B: Identify high-throughput markers for important traits. Sub-objective 2.C: Conduct collaborative development of genomic selection models for prediction of yield, agronomic traits, and grain quality and evaluate prediction accuracy. Objective 3: Increase knowledge of the molecular basis for virulence and resistance for leaf rust and Hessian fly, and tolerance to heat stress in wheat. Sub-objective 3.A: Identify mechanisms of virulence and resistance for leaf rust. Sub-objective 3.B: Identify mechanisms of virulence and resistance for Hessian fly. Sub-objective 3.C: Identify mechanisms of tolerance for heat stress.

Production of hard winter wheat is limited by recurring intractable problems such as diseases, insects, heat stress, and drought stress. In addition, emerging problems, such as Ug99 stem rust, threaten the sustainability of production. The first objective of this project is to identify and develop adapted hard winter wheat germplasm with improved resistance to leaf rust, yellow rust, stem rust, Hessian fly, Fusarium head blight, and tolerance to heat and drought stress. We will identify sources of resistance, transfer the resistance genes into adapted backgrounds, identify linked markers, validate the gene effects, and release new germplasm lines for cultivar development. The second objective is to develop more efficient wheat breeding techniques based on high throughput phenotyping and genotyping methods as well as genomic selection models. High-throughput phenotyping platforms will be developed using proximal sensing and georeferenced data collection for rapid assessment of field plots. Genotyping-by-sequencing will be used to characterize genome-wide molecular markers on breeding material and apply genomic selection in wheat breeding. New high-throughput markers will be developed for marker-assisted selection of traits of interest. The third objective is to increase our knowledge of the molecular basis for virulence/avirulence and resistance for leaf rust and Hessian fly, and tolerance to heat stress in wheat. Greater understanding of avirulence effectors in the Hessian fly and the leaf rust pathogen may lead to better strategies for durable resistance. Likewise, uncovering the mechanisms of abiotic stress tolerance may lead to discovery of new tolerance genes with improved or complementary effects.

Progress Report
Objective 1. All data have been collected and analysis is in progress for minor gene resistance to stem rust, leaf rust, and stripe rust in the cultivars ‘Kingbird’ and ‘Roelfs F2007’. The combination of major stem rust resistance genes Sr22, Sr26, Sr35, Sr38/Yr17, and Sr57/Lr34 is being backcrossed into elite germplasm lines from several cooperating breeding programs. For alien genes Sr22, Sr26, and Sr35, we are using the shortest alien chromosome segments available to reduce the chances of negatively affecting yield or quality. Several winter wheat lines with new sources of rust resistance will be tested in the coming year for disease resistance, yield, and grain quality for potential release as new parents for wheat breeding programs. We are initiating crosses to characterize and move several new sources of resistance to stripe rust into adapted winter wheat lines. 5,325 wheat lines were screened for resistance to stripe rust in an inoculated field nursery at Rossville, KS. The test included the Southern Regional Performance Nursery (SRPN), Northern Regional Performance Nursery (NRPN), and Regional Observation Nursery (RGON) regional germplasm nurseries as well as entries from 15 cooperators and three mapping populations. We screened 5,312 wheat lines for Hessian fly resistance this year in greenhouse tests. Results were used by geneticists to map new sources of resistance and by breeders to select new cultivars with resistance to Hessian fly. Fhb1, an important Fusarium head blight resistance gene, has been transferred into 11 locally adapted hard winter wheat lines from five states using marker-assisted backcrossing and doubled haploid techniques. About 500 Fhb1 pure lines were developed and sent to 6 breeding programs for further evaluation and breeding activities. Two new populations were developed for mapping the locations of new genes for Fusarium head blight resistance. Genes for tolerance to post-flowering heat stress in wheat are being investigated in three mapping populations between tolerant and susceptible lines. Genes for tolerance are also being sought in two association mapping panels of diverse winter wheat lines or spring wheat lines. More than 10,000 wheat breeding samples from 10 breeding programs were analyzed for molecular markers in the USDA-ARS Central Small Grains Genotyping Laboratory. The SRPN and NRPN regional wheat nurseries were also characterized with more than 60 gene-specific markers linked to important traits of interest to breeders. A total of over 50,000 gene-specific marker data points were generated in 2016. In addition, over 30,000,000 genome-wide GBS marker data points were generated for wheat and rye. The data were used by wheat researchers for characterizing and selecting breeding lines with desired combinations of agronomic and pest resistance traits. Objective 2. We developed a new diagnostic marker for the Fhb1 resistance gene for Fusarium head blight in wheat based on a new candidate gene for Fhb1. The new marker has better sensitivity and specificity than any other marker for Fhb1. Most public sector winter wheat breeding programs in the Great Plains have adopted the Wheat Workers’ Material Transfer Agreement (MTA) to facilitate the exchange of germplasm while protecting the intellectual property of the originating institution. We led the effort for ARS adoption of the Wheat Workers’ MTA, which has streamlined and standardized the process for accessing germplasm from public sector breeding programs, as well as provided a standardized mechanism for distributing ARS germplasm to public sector wheat breeding programs. We are working to establish CRADA-MTAs with several Land Grant institutions to provide an intellectual property framework for ARS scientists to use the most elite wheat germplasm from public sector breeding programs as the genetic background into which new resistances to diseases, insects, and climate stress can be introduced and evaluated. We are developing the Ms3 male-sterile gene as a tool to assist in rapidly backcrossing multiple new desirable genes into elite wheat backgrounds. The presence of the dominant Ms3 sterility gene in the female parent removes the need for tedious work to remove the anthers by hand from the designated female spikes when making crosses. This will allow researchers to quickly and easily produce large numbers of hybrid seeds during backcrossing, thus increasing the chances of obtaining desired combinations of new genes in the progeny. Objective 3. Virulent mutants of the leaf rust fungus, created using fast neutron bombardment, were identified for wheat leaf rust resistance genes Lr2A, Lr2C, Lr11, and Lr26. Virulent mutants are expected to have new mutations in the avirulence effector genes that condition resistance when interacting with host plant resistance genes. Genomic sequence comparisons of mutants will be performed to identify candidate genes for the avirulence effector genes. Identifying and characterizing the effectors in the leaf rust fungus is considered to be a key to designing more durable resistance. Another key to durable resistance could be to identify the susceptibility genes to leaf rust in wheat. The susceptible spring wheat variety Thatcher was treated with the mutagen EMS to create a population of 3500 mutant lines. These lines will be screened for expression of resistance to the leaf rust pathogen. Resulting resistant lines may have mutations in genes that control susceptibility to the pathogen. Such lines will be characterized to identify candidate susceptibility genes.

1. Novel mechanism of resistance to Triticum mosaic virus in wheat. In wheat, Triticum mosaic virus (TriMV) causes mosaic symptoms in the leaves, causes the plants to be stunted, and can cause significant reductions in yield. There are only a few sources of resistance to TriMV, so novel sources of resistance are needed. ARS researchers in Manhattan, Kansas added a fragment of the TriMV virus coat protein sequence to the wheat genome. The sequence was designed in such a way that caused the plant to deactivate the virus using a mechanism called RNA interference. Plants were found to be resistant to the virus and to maintain resistance for at least six generations. Further testing is needed before this type of resistance can be used in commercial wheat cultivars, but this work shows that the method has great promise for controlling wheat virus diseases.

2. Gene for kernel size in wheat identified. Thousand-kernel weight (TKW) is one of the major components of grain yield in wheat. ARS researchers in Manhattan, Kansas mapped a gene for high TKW in wheat cultivar ‘Clark’. This gene explained 19.7% of variation for TKW and also showed a major effect on kernel length. Two closely linked DNA markers for the gene were validated in a diversity panel of 200 U.S. winter wheat accessions. Breeder-friendly markers were developed that can be used to improve wheat kernel size.

3. Molecular markers developed for resistance to Fusarium head blight in wheat. Wheat Fusarium head blight (FHB) is an important disease of wheat. Use of DNA markers tightly linked to resistance genes can significantly improve the selection efficiency in breeding. ARS researchers in Manhattan, Kansas evaluated 192 wheat accessions for FHB in three field experiments, and genotyped them using 364 markers. Among those markers, 11 showed significant relationships with FHB severity. Mean FHB severities were negatively correlated with the number of favorable markers. Thus, selection for favorable markers should result in higher levels of FHB resistance in breeding materials without the time and expense of multi-year field testing.

4. Molecular markers developed for wheat grain quality. Wheat grain quality traits define the value and potential end-use products of a wheat cultivar. ARS researchers in Manhattan, Kansas and collaborators genetically mapped the genes controlling grain quality in a population derived from the cross of wheat cultivars ‘Ning7840’ and ‘Clark’. The population was evaluated for quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 genes with additive effects on different quality traits was identified. The findings shed light on the inheritance of wheat grain quality traits and provided DNA markers for manipulating these important traits to improve quality of new wheat cultivars.

5. Multiplex assay developed for high throughput analysis of genetic markers in wheat. The majority of genetic markers in wheat are currently tested in single marker assays. Multiplex assays that simultaneously analyze many markers in one assay will reduce marker assay cost and time, and increase breeding efficiency. ARS researchers in Manhattan, Kansas successfully multiplexed 27 markers and results were comparable to the corresponding single marker analyses. The multiplexed assay is suitable for rapid and high-throughput screening of genetic markers in wheat.

6. Validation of new method to genetically anchor and order plant genome assemblies. POPSEQ is a new method to genetically anchor and order plant genome assemblies based on low-coverage sequencing of the DNA of progeny from a cross between two diverse parents. ARS researchers in Manhattan, Kansas and university colleagues compared the alignment of the POPSEQ method with standard linkage mapping methods for a reference population. The results showed strong agreement between the independent new linkage map and the POPSEQ mapping approach, thus validating the POPSEQ method. In addition to anchoring plant genome assemblies, the POPSEQ-based ordering method enables the application of unordered markers to gene mapping and breeding in wheat without the need for creating new linkage maps for each study.

7. New tool for genetic analysis of Hessian fly of wheat. Hessian fly is a destructive pest of wheat that typically overcomes wheat resistance within 3-8 years after the initial deployment of a new resistance gene. To develop wheat cultivars with more durable resistance, we need new tools to identify the genetic factors in Hessian fly that can trigger resistance in the wheat host. ARS researchers in Manhattan, Kansas applied a new technology called genotyping-by-sequencing to individual Hessian flies. The method resulted in more than 7000 new DNA markers for the Hessian fly genome. The new markers can be used for genetic analysis of the factors in Hessian fly that control virulence and resistance.

8. Two new wheat cultivars and one germplasm line were co-developed by ARS and university collaborators. New wheat cultivars are needed by producers to increase yield potential and grain quality as well as tolerance to diseases and insects. In collaboration with Oklahoma State University, Kansas State University, and the University of Nebraska, ARS researchers in Manhattan, Kansas participated in the development and registration of three new wheat cultivars or germplasm lines for the Great Plains including wheat lines ‘OK05312’, ‘Joe’, and ‘Panhandle’. Germplasm line OK05312 will be valuable as a breeding parent that carries resistance to the wheat curl mite, which transmits wheat streak mosaic virus and Triticum mosaic virus. Joe and Panhandle are new wheat cultivars that are expected to produce higher and more consistent yields for producers in the Great Plains region of the U.S.


Review Publications
Segovia, V., Bruce, M.A., Shoup-Rupp, J.L., Huang, L., Bakkeren, G., Trick, H.N., Fellers, J.P. 2016. Two small secreted proteins from Puccinia triticina induce reduction of ß-glucoronidase transient expression in wheat isolines containing Lr9, Lr24, and Lr26. Canadian Journal of Plant Pathology. doi:10.1080/07060661.2016.1150884.
Baenziger, S.P., Graybosch, R.A., Regassa, T., Klein, R.N., Kruger, G.R., Santra, D.K., Rose, D.J., Wegulo, S.N., Jin, Y., Kolmer, J.A., Hein, G.L., Chen, M., Bai, G., Bowden, R.L., Poland, J.A. 2016. Registration of ‘NE05548’ (husker genetics brand panhandle) hard red winter wheat. Journal of Plant Registrations. 10(2). doi:10.3198/jpr2016.01.0006crc.
Su, Z., Jin, S., Yue, L., Zhang, G., Chao, S., Bai, G. 2016. Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat. Molecular Breeding. 36: 15. doi:10.1007/s11032-016-0436-4.
Luo, M., Zhang, D., Wu, D., Li, L., Bai, G. 2016. Effective marker alleles associated with type II resistance of wheat to Fusarium head blight infection in fields. Journal of Breeding Science. doi: 10.1270/jsbbs.15124.
Kolmer, J.A., Lagudah, E.S., Lillemo, M., Lin, M., Bai, G. 2015. The Lr46 gene conditions partial adult-plant resistance to yellow rust, stem rust, and powdery mildew in Thatcher wheat. Crop Science. 55:2557-2565. doi: 10.2135/cropsci2015.02.0082.
Bernardo, A., Wang, S., St Amand, P.C., Bai, G. 2015. Using Next Generation Sequencing for Multiplexed Trait-linked Markers in Wheat. PLoS One. 10(12):e0143890. doi:10.1371/journal.pone.0143890.
Li, G., Xu, X., Bai, G., Carver, B.F., Hunger, R.M., Bonman, J.M. 2016. Identification of novel powdery mildew resistance sources in wheat. Crop Science. 56(4):1817-1830.
Fakthongphan, J., Graybosch, R.A., Bai, G., St Amand, P., Baenziger, S.P. 2015. Identification of markers linked to genes for sprouting tolerance (independent of grain color) in hard white winter wheat (HWWW). Theoretical and Applied Genetics. PP 1-12.
Das, M.K., Bai, G., Mujeeb-Kazi, A., Rajaram, S. 2015. Genetic diversity among synthetic hexaploid wheat accessions with resistance to several fungal diseases. Genetic Resources and Crop Evolution. doi:10.1007/s10722-015-0312-9.
Li, C., Bai, G., Carver, B., Chao, S., Wang, Z. 2015. Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat. The Crop Journal. (2016) 4: 1-11.
Xu, X., Bai, G. 2015. Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery. Molecular Breeding. 35(1):33.
Tao, L., Dadong, Z., Xiali, Z., Bai, G., Lei, L., Shiliang, G. 2015. Fusarium head blight resistance loci in a stratified population of wheat landraces and varieties. Euphytica. 207:551. doi:10.1007/s10681-015-1539-4.
Liu, S., Sehgal, S.K., Lin, M., Li, J., Trick, H., Gill, B., Bai, G. 2015. Independent mis-splicing mutations in TaPHS1 causing loss of pre-harvest sprouting (PHS) resistance during wheat domestication. New Phytologist. 208(3):928-35. doi:10.1111/nph.13489.
Dunckel, S.M., Olson, E.L., Rouse, M.N., Bowden, R.L., Poland, J.A. 2015. Genetic mapping of race-specific stem rust resistance in the synthetic hexaploid W7984 x Opata M85 mapping population. Theoretical and Applied Genetics. 55:1–9. doi: 10.2135/cropsci2014.11.0755.
Edae, E.A., Bowden, R.L., Poland, J.A. 2015. Application of population sequencing (POPSEQ) for ordering and inputting genotyping-by-sequencing markers in hexaploid wheat. G3, Genes/Genomes/Genetics. 5(12):2547- 2553. doi:10.1534/g3.115.020362.
Liu, M., Lei, L., Powers, C., Lu, Z., Campbell, K., Chen, X., Bowden, R.L., Carver, B., Yan, L. 2015. TaXA21-A1 on chromosome 5AL is associated with resistance to multiple pests in wheat. Theoretical and Applied Genetics. 129:345-355. doi:10.1007/s00122-015-2631-9.
Chen, M., Liu, S., Wang, H., Cheng, X., El Bouhssini, M., Whitworth, R.J. 2016. Massive shift in gene expression during transitions between developmental stages of the Gall Midge, Mayetiola destructor. PLoS One. 11(5): e0155616. doi:10.1371/journal.pone.0155616.
Shoup Rupp, J.L., Cruz, L.F., Trick, H.N., Fellers, J.P. 2016. RNAi mediated, stable resistance to Triticum mosaic virus in wheat. Crop Science. 56(4):1602-1610.
Wang, Z., Cai, J., Bai, G., Whitworth, J.R., Wang, H., Shukle, R.H., Stuart, J.J., Chen, M. 2016. Analysis of Single Nucleotide Polymorphism via Genotyping-by-Sequencing in the Gall Midge Mayetiola Destructor (Hessian Fly). Scientific Reports. 84 (2016) 22-31.
Bai, G., Li, C., Carver, B., Chao, S., Wang, Z. 2016. Mapping quantitative trait loci for plant adaptation and morphology traits in wheat using single nucleotide polymorphisms. Euphytica. 208:299-312. doi:10.1007/s10681-015-1594-x.
Zhang, X., Bai, G., Xu, R., Guorong, Z. 2015. Wheat streak mosaic virus resistance in eight wheat germplasm lines. Plant Breeding Reviews. 135(1):26-30. doi:10.1111/pbr.12334.
Li, C., Bai, G., Chao, S., Wang, Z. 2016. A high-density SNP and SSR consensus map reveals segregation distortion regions in wheat. BioMed Research International. doi:10.1155/2015/830618.
Zhao, C., Shukle, R.H., Navarro Escalante, L., Chen, M., Richards, S., Stuart, J.J. 2015. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family. Journal of Insect Physiology. 84:22-31. doi:10.1016/j.jinsphys.2015.10.001.
Schwarting, H.N., Whitworth, R., Chen, M., Cramer, G., Maxwell, T. 2016. Impact of hessian fly, Mayetiola destructor, feeding on selected developmental aspects of hard red winter wheat in Kansas. Southwestern Entomologist. 41(2):321-330. doi:10.3958/059.041.0208.
Cooper, J.K., Stromberger, J.A., Morris, C.F., Bai, G., Haley, S.D. 2016. End-use quality and agronomic characteristics associated with the Glu-B1al high-molecular-weight glutenin allele in U.S. hard winter wheat. Crop Science. 56:1-6.
Schwarting, H., Whitworth, R., Cramer, G., Chen, M. 2015. Pheromone trapping to determine Hessian fly (Diptera: Cecidomyiidae) activity in Kansas. Journal of Kansas Entomological Society. 88(4):411-417. doi:10.2317/0022-8567-88.4.411.
Kalia, B., Wilson, D.L., Bowden, R.L., Singh, R.P., Gill, B.S. 2016. Adult plant resistance to Puccinia triticina in a geographically diverse collection of Aegilops tauschii. Genetic Resources and Crop Evolution. doi:10.1007/s10722-016-0411-2.
Zhang, G., Martin, T.J., Fritz, A.K., Miller, R., Chen, M., Bowden, R.L., Bai, G. 2016. Registration of ‘Joe’ hard white winter wheat. Journal of Plant Registrations. doi:10.3198/jpr2016.02.0007crc.
Li, L., Shi, X., Zheng, F., Li, C., Wu, D., Bai, G., Gao, D., Wu, J., Li, T. 2016. A novel nitrogen-dependent gene associates with the lesion mimic trait in wheat. Journal of Theoretical and Applied Genetics. doi:10.1007/s00122-016-2758-3.
Kumssa, T., Zhao, D., Bai, G., Zhang, G. 2016. Resistance to wheat streak mosaic virus and Triticum mosaic virus in wheat lines carrying Wsm1 and Wsm3. European Journal of Plant Pathology. doi:10.1007/s10658-016-1021-8.
Carver, B., Smith, C., Chuang, W., Hunger, R.M., Edwards, J.T., Yan, L., Brown Guedira, G.L., Gill, B.S., Bai, G., Bowden, R.L. 2015. Registration of OK05312, a high-yielding hard winter wheat donor of Cmc4 for wheat curl mite resistance. Journal of Plant Registrations. 10:75-79 doi:10.3198/jpr2015.04.0026crg.