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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF HARD RED SPRING AND DURUM WHEAT FOR DISEASE RESISTANCE AND QUALITY USING GENETICS AND GENOMICS

Location: Cereal Crops Research

2013 Annual Report


1a. Objectives (from AD-416):
Identify novel sources of resistance to Fusarium head blight (FHB), Stagonospora nodorum blotch (SNB), tan spot (TS), stem rust (SR) and Hessian fly (HF) among accessions of the primary gene pool of wheat. Develop and characterize synthetic hexaploid wheat lines, genetic stocks, and mapping populations useful for the genetic analysis of resistance to FHB, SNB, TS, SR, and HF. Identify novel QTL associated with resistance to FHB, SNB, TS, and end-use quality in tetraploid and/or hexaploid mapping populations. Isolate genes associated with host-pathogen interactions involving host-selective toxins produced by the SNB and TS pathogens. Conduct genomic analysis and fine mapping of genomic regions harboring genes conferring sensitivity to host-selective toxins and for Hessian fly resistance, and develop markers suitable for marker-assisted selection. Introgress genes/QTL for resistance to FHB, SNB, and TS into adapted germplasm using marker-assisted selection. Develop small grains germplasm and varieties with improved disease resistance and end-use quality using high-throughput genotyping and marker-assisted selection.


1b. Approach (from AD-416):
Survey tetraploid relatives of wheat for resistance to FHB, SNB, TS, SR, and HF. Develop synthetic hexaploid lines, near-isogenic lines, and mapping populations using conventional techniques. Develop genetic linkage maps in the segregating mapping populations using molecular markers and identify genomic regions harboring QTL associated with resistance or improved quality. Use QTL analysis to determine the chromosomal locations of genes governing resistance and quality traits. Target genomic regions harboring disease resistance loci, sensitivity to host-selective toxins, and Hessian fly resistance with PCR-based markers to identify markers suitable for marker-assisted selection. Isolate the Tsn1 gene using positional cloning techniques. Develop a high-resolution map of the H26 gene for genomic analysis and positional cloning. Develop improved germplasm through the use of conventional and marker-assisted selection. Release enhanced germplasm to wheat breeders and deposit germplasm stocks in the National Germplasm System. Utilize high-throughput marker platforms for genotyping lines for the small grains breeding community, and develop new high-throughput markers for important agronomic traits. BL-1; 04/04/08


3. Progress Report:
This is the final report for the project 5442-21000-033-00D. Research continues under the new project 5442-21000-037-00D. Significant progress was made over the life of the project and the following is a summary of that progress. Common and durum wheat populations were evaluated for reaction to the fungal disease tan spot. Molecular marker analysis revealed multiple genes in each population associated with tan spot resistance. The markers were used to develop germplasm with improved tan spot resistance. Several novel genes that govern susceptibility to the fungal disease Stagonospora nodorum blotch (SNB) were identified in wheat. The roles of these genes in disease development were quantified and the isolation of one of the genes provided extensive knowledge regarding the mechanisms involved in the plant-pathogen interaction. Molecular markers were developed for each gene and used to develop germplasm with enhanced SNB resistance. Various genetic stocks were developed, characterized, and provided to other researchers for genetic studies upon request. The genetic stocks include chromosome substitution lines, near-isogenic lines and genetically engineered lines. Various novel Ug99 stem rust resistance genes were transferred from goatgrass accessions to wheat using novel chromosome engineering methods and characterized for use in germplasm development. Markers were developed for most of the stem rust resistance genes to aid in their transfer to common wheat varieties. Novel seed storage proteins and bread making end-use quality traits were discovered and characterized in various wheat lines. The genes will be useful for the improvement of end-use quality and enhancement of nutritional value. Novel genes conferring high levels of resistance to Fusarium head blight were discovered. Molecular markers associated with the genes were identified and shown to be useful for the efficient deployment of the resistance genes. Germplasm containing the novel Fusarium head blight resistance genes has been provided to breeders for use in breeding programs. Genes governing wheat domestication were characterized at the molecular level. This work provides useful knowledge regarding wheat domestication, development, and genetic regulation of complex traits that will help researchers devise strategies to increase wheat yields and productivity in the future. High-density single nucleotide polymorphism (SNP) markers were developed, evaluated, and implemented in genotyping assays for wheat, barley, and oat. These markers and marker panels offer extremely high-throughput capabilities for genome mapping and the characterization of breeding materials, allowing efficient selections to be made and rapid development of superior varieties. A family of pathogenesis-related genes was characterized at the molecular level in wheat. The knowledge gained in this work allows researchers to understand the roles of these genes in governing disease resistance and may lead to new methods for breeding and engineering disease resistant crops.


4. Accomplishments


Review Publications
Lu, S., Edwards, M.C., Friesen, T.L. 2013. Genetic variation of single nucleotide polymorphisms identified at the mating type locus correlates with form-specific disease phenotype in the barley net blotch fungus Pyrenophora teres. European Journal of Plant Pathology. 135(1):49-65.

Lu, S., Faris, J.D., Sherwood, R., Edwards, M.C. 2013. Dimerization and protease resistance: new insight into the function of PR-1. Journal of Plant Physiology. 170:105-110.

Chen, J., Chu, C., Souza, E.J., Guttieri, M.J., Chen, X., Xu, S.S., Hole, D., Zemetra, R. 2011. Genome-wide identification of QTLs conferring high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici) in wheat. Molecular Breeding. DOI:10.1007/s11032-011-9590-x.

Olivera, P., Babebo, A., Xu, S.S., Klindworth, D.L., Jin, Y. 2012. Resistance to race TTKSK of Puccinia graminis f. sp. tritici in Emmer Wheat (Triticum turgidum ssp. dicoccum). Crop Science. 125:817–824.

McArthur, R.I., Zhu, X., Oliver, R.E., Klindworth, D.L., Xu, S.S., Stack, R.W., Wang, R., Cai, X. 2012. Homoeology of Thinopyrum junceum and Elymus rectisetus chromosomes to wheat and disease resistance conferred by the Thinopyrum and Elymus chromosomes in wheat. Chromosome Research. 20:699-715.

Akhunov, E.D., Sehgal, S., Liang, H., Wang, S., Akhunova, A.R., Kaur, G., Li, W., Forrest, K.L., See, D., Simkova, H., Ma, Y., Hayden, M.J., Luo, M., Faris, J.D., Dolezel, J., Gill, B.S. 2013. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiology. 161:252-265.

Faris, J.D., Abeysekara, N.S., McClean, P.E., Xu, S.S., Friesen, T.L. 2012. Tan spot susceptibility governed by the Tsn1 locus and race-nonspecific resistance quantitative trait loci in a population derived from the wheat lines Salamouni and Katepwa. Molecular Breeding. 30:1669-1678.

Klindworth, D.L., Hareland, G.A., Elias, E.M., Xu, S.S. 2013. Attempted compensation for linkage drag affecting agronomic characteristics of durum wheat 1AS/1DL translocation lines. Crop Science. 53:422-429.

Cavanagh, C., Chao, S., Wang, S., Huang, B.E., Stephan, S., Kiani, S., Forrest, K., Saintenac, C., Brown Guedira, G.L., Akhunova, A., See, D.R., Bai, G., Pumphrey, M.O., Tomar, L., Wong, D., Kong, S., Reynolds, M., Lopez Da Silva, M., Bockelman, H.E., Talbert, L., Anderson, J.A., Dreisigacker, S., Baenziger, S., Carter, A., Korzun, V., Morrell, P.L., Dubcovsky, J., Morell, M., Sorrells, M., Hayden, M., Akhunov, E. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landrace and cultivars. Proceedings of the National Academy of Sciences. 110:8057-8062.

Kumar, A., Simons, K., Iqbal, M.J., Jimenez, M., Bassi, F.M., Ghavami, F., Al, A., Wang, Y., Luo, M., Gu, Y.Q., Denton, A., Xu, S.S., Dvorak, J., Kianian, P., Kianian, S.F. 2012. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii. Biomed Central (BMC) Genomics. 13:597.

Oliver, R.E., Tinker, N.A., Lazo, G.R., Chao, S., Jellen, E.N., Carson, M.L., Rines, H.W., Obert, D., Lutz, J.D., Shackelford, I., Korol, A.B., Wight, C., Gardner, K.M., Hattori, J., Beattie, A., Bjornstad, A., Bonman, J.M., Jannink, J., Mitchell Fetch, J.W., Harrison, S., Howarth, C.J., Ibrahim, A., Kolb, F.L., McMullen, M.S., Murphy, J.P., Ohm, H., Rossnagel, B.G., Yan, W., Miclaus, K.J., Hiller, J., Maughan, P.J., Redman-Hulse, R.R., Anderson, J.M., Islamovic, E., Jackson, E.W. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One. 8:e58068.

Last Modified: 10/19/2017
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