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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
1. Development of DNA-based tools to accelerate the development of superior varieties of small grains. DNA markers along a genome are like landmarks along a highway, and the markers can be used during the development of new varieties to select segments of the genome that contain desirable genes. However, small grains like wheat and barley have extremely large genomes making it necessary to have a large number of markers to achieve adequate density for selection of the desirable genes. ARS scientists in Fargo, ND, in collaboration with other scientists in the US and elsewhere, developed high-density DNA marker panels that allow up to 92,000 markers distributed throughout the genome to be evaluated at once. The high-density marker panels can be used to evaluate a large number of lines at a low cost and will enable US small grains breeders to more rapidly and efficiently develop varieties with superior performance and quality.

2. Development and characterization of new wheat lines for disease resistance. Wheat lines developed by crossing durum wheat with a wild wheat relative known as goatgrass are referred to as synthetic lines. Synthetic lines are useful for crossing with established wheat lines and varieties for improving disease resistance. ARS researchers in Fargo, ND developed 200 new synthetic lines and evaluated 80 of them for resistance to four major wheat diseases including stem rust, stripe rust, tan spot, and Stagonospora nodorum blotch. The results indicated that a number of the synthetic lines carried unique genes for resistance. These lines should therefore prove valuable for the improvement of disease resistance in wheat.

3. Development of wheat lines carrying a stem rust resistance gene derived from tall wheatgrass. The stem rust resistance gene known as Sr43 was previously transferred from tall wheatgrass into wheat, and it is effective against major races of stem rust, including Ug99. However, previous studies indicated that Sr43 was associated with nearby deleterious genes also from tall wheatgrass, making the wheat lines with Sr43 unsuitable for use in wheat varietal development. ARS researchers in Fargo, ND applied a recently established chromosome engineering procedure to disassociate Sr43 from the nearby deleterious tall wheatgrass genes. As a result, two new wheat lines carrying Sr43, but far fewer other tall wheatgrass genes, were developed. Two DNA markers associated with Sr43 were also identified. The two new wheat lines with Sr43 and the DNA markers provide new resources for improving wheat for resistance to Ug99 and other races of stem rust.

4. Identification and characterization of genes for tan spot resistance. Tan spot is a serious fungal disease of wheat that causes significant yield losses. Because the utilization of tan spot-resistant cultivars is an effective approach for reducing losses, wheat breeders need new sources of tan spot resistance to incorporate into new varieties. ARS researchers in Fargo, ND, conducted genetic analyses of a primitive wheat variety and found that it contained four tan spot resistance genes. Only one of the genes was previously known, and the remaining three were newly discovered. The resistance genes and molecular markers can be used to develop durum and bread wheat cultivars with improved tan spot resistance.

5. Identification and characterization of genes for Stagonospora nodorum blotch resistance. Stagonospora nodorum blotch (SNB) is a devastating fungal pathogen of wheat that causes significant yield losses. The use of SNB resistant wheat varieties is the best way to reduce losses, thereby making the identification of SNB resistance genes critical for use in varietal development. ARS researchers in Fargo, ND conducted genetic analyses of two resistant and two susceptible wheat lines and found four genes associated with the development of SNB. The results indicated that the four genes were present in the susceptible wheat lines and actually caused susceptibility to the disease, whereas the other two lines were resistant because they lacked the susceptibility genes. The molecular markers found to be associated with the susceptibility genes will be useful for wheat breeders to efficiently remove the susceptibility genes from breeding lines.

6. Characterization of wheat proteins involved in response to disease. Proteins belonging to a class known as pathogenesis-related, or PR proteins, are believed to play roles in plant defense against invading pathogens. However, exactly how PR proteins help to defend against pathogens is yet unknown. ARS researchers in Fargo, ND, conducted experiments on two wheat PR proteins and found that they are resistant to certain protein degrading enzymes and have similarities to human caspase proteins, which are essential for a healthy immune system and have cancer-fighting properties. These findings indicate that PR proteins may contribute to disease resistance in plants through mechanisms similar to those of caspases in humans. This discovery provides new insights to the molecular mechanisms of plant defense, and may lead to novel strategies to develop disease resistant wheat varieties.

7. Assessment of yield loss associated with incorporation of a bread wheat DNA segment into durum wheat. Durum wheat, which is used to make pasta products, lacks a gene for good bread-making quality in a chromosome that is uniquely present in bread wheat. Incorporation of the gene from bread wheat into durum wheat would make durum suitable for making bread, but the bread wheat DNA segment carrying the gene usually causes yield reductions in durum wheat. To measure yield loss associated with incorporation of the bread wheat DNA segment into durum wheat, and to identify potential genetic backgrounds that can mitigate the yield losses, ARS researchers in Fargo, ND incorporated the segment into six durum cultivars. The result from yield trials showed that the segment decreased yield in all of the cultivars, with losses ranging from 7.0 to 20.5%. However, the durum variety Lebsock was found to have significantly less yield loss than the others, indicating that the Lebsock genetic background partially compensated for the presence of the bread wheat DNA segment. This knowledge will allow durum wheat breeders to minimize yield loss potential when incorporating useful genes from bread wheat into durum.


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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Last Modified: 9/22/2014
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