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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
2012 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:
A population of recombinant inbred lines derived from the hexaploid wheat lines Salamouni and Katepwa was screened for reaction to tan spot and Stagonospora nodorum blotch, and over 400 molecular markers were used to genotype the population and assemble genetic linkage maps of all 21 chromosomes. Analysis of the data is in progress and will lead to the identification of novel genes and quantitative trait loci associated with tan spot and Stagonospora nodorum blotch resistance. This work relates directly to sub-objective 2C.

Differential expression analysis of the pathogenesis-related protein 1 (PR-1) gene family in wheat plants infected with the stem rust fungus indicated that fifteen Pr-1 genes were expressed with a majority showing patterns distinguishable between resistant and susceptible wheat lines. Several Pr-1 genes were found to be rust-inducible only in the resistant line. Additional analysis to determine the importance of these PR-1 genes is in progress. This work directly relates to sub-objective 2D.

Functional characterization of PR-1 proteins indicated that two pathogen-inducible PR-1 proteins were resistant to proteases. Site-specific mutations revealed that dimerization of the PR-1 protein relates to the protease resistance. Conserved signature sequences were found in PR-1 and human apoptosis-related proteins. Further analysis is in progress to determine if PR-1 contributes to programmed cell death-mediated disease resistance in plants. This work directly relates to sub-objective 2D.

Towards development of hard red spring wheat near-isogenic lines for genes conferring sensitivity to host-selective toxins produced by Stagonospora nodorum, the four lines used as donors of Tsn1, Snn1, Snn2, and Snn3 were backcrossed to BR34 as the recurrent parent, respectively. The BC4F1 progeny from each of backcrosses were directly evaluated for reactions to respective toxins and BC5F1 progeny for the four genes were produced. This work relates directly to sub-objective 1C.

For introgression of Fusarium head blight resistance from cultivated emmer and Persian wheat into durum wheat, two emmer (PI 41025 and PI 272527) and Persian wheat accessions (PI 61102 and PI 94748), and a hexaploid wheat line (PI 277012) with FHB resistance were previously backcrossed to durum wheat cultivars. Seven BC1-derived advanced lines and one double haploid with improved FHB resistance were selected and backcrossed with the new durum cultivar ‘Tioga’ and two elite durum lines (D03028 and D04581). Approximately 2,000 BC1F1 plants and their progenies were evaluated in greenhouse and field nurseries. This work relates directly to sub-objective 3A.

Genetic mapping analysis of end-use quality traits was carried out to detect major QTL having large genetic effects on 20 quality traits evaluated. A total of 31 chromosomal regions containing genes affecting these traits were identified. The results provided better knowledge of the inheritance of the quality traits in spring wheat adapted to the Northern Plains regions.


4.Accomplishments
1. Introduction of stem rust Ug99 resistance genes into wheat. Stem rust race Ug99 has the potential to devastate world wheat production. Goatgrass is a wild relative of wheat that has genes conferring good levels of resistance to Ug99, but these resistance genes are difficult to introduce into cultivated wheat. ARS researchers in Fargo, ND and St. Paul, MN used chromosome engineering techniques to successfully transfer small segments of goatgrass chromosomes carrying the Ug99-resistance gene (Sr47) to durum wheat. Molecular markers that can be used to select the goatgrass chromosomal segment carrying the rust resistance gene were also identified. Durum wheat lines carrying Sr47 and the molecular markers developed in this research provide useful resources for developing wheat varieties with resistance to Ug99 and other stem rust races.

2. Identification and characterization of two genes for Fusarium head blight resistance. Fusarium head blight (FHB) is a serious fungal disease that currently threatens wheat production in the U.S. Because the utilization of FHB-resistant cultivars is an effective approach for protecting wheat against FHB, new sources of FHB resistance have been in high demand by wheat breeders. ARS researchers in Fargo, ND, in cooperation with North Dakota State University scientists, identified a wheat line (PI 277012) with a high level of FHB resistance. Based on genetic analysis, they identified two major FHB resistance genes, one of which was not previously reported. The major FHB resistance genes and molecular markers are being used for developing durum and bread wheat cultivars with improved FHB resistance in several breeding programs.

3. The evolution of genes governing the domestication of modern bread wheat. The wheat gene 5AQ is known to play a major role in wheat domestication and has been studied extensively, but two additional forms, known as 5Bq and 5Dq, exist in wheat and have not been investigated. ARS researchers in Fargo, ND, determined that the 5Dq gene more closely resembles 5AQ than does 5Bq, but both 5Bq and 5Dq contribute to wheat domestication through an intricately regulated network involving all three genes. It was also determined that, once wheat was domesticated, the 5AQ gene was transformed to a hyperfunctionalized state and became a master regulatory switch, whereas the effects of the other two genes were reduced in comparison. 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.

4. Toxin expression and severity of wheat fungal disease. The fungal pathogen Stagonospora nodorum is a serious pathogen of wheat. Many strains of S. nodorum produce a toxin known as ToxA, but the strains differ in their ability to cause disease; the underlying mechanism(s) for strain differences is unknown. ARS researchers in Fargo, ND, determined that different ToxA-producing strains of the S. nodorum pathogen express the ToxA encoding gene at different levels. The levels of ToxA expression were highly correlated with disease severity of infected plants, suggesting that increased levels of toxin production leads to more disease. This research provides insights into how wheat pathogens may be manipulated to enhance the disease resistance of wheat.

5. Identification and marker analysis of Hessian fly-resistance genes in wheat. Synthetic hexaploid wheat (SHW) lines are excellent sources of resistance genes for diseases and insects in wheat, and they have been widely used in wheat breeding and genetic studies. Some of these lines may harbor resistance to Hessian fly, a serious insect pest for wheat in the U.S. ARS researchers in Fargo, ND, in cooperation with North Dakota State University scientists, evaluated 118 elite SHW lines for resistance to Hessian fly and identified 52 SHW lines with high or moderate levels of resistance. Based on marker analyses, it is predicted that 19 of the resistant lines carry novel Hessian fly-resistance genes. The resistant SHW lines identified in this study should be useful for development of resistant cultivars and for genetic and evolutionary studies of resistance genes.

6. Development of a DNA marker panel for oats. The development of useful DNA markers for oat has been lacking due in large part to the complex structure of the oat genome. An ARS scientist in Fargo, ND, in collaboration with oat scientists in the US, evaluated over 6,000 DNA markers and investigated the genetic diversity among a set of oat varieties from around the world. These results contributed to the production of a high-density DNA marker panel containing 6,000 DNA markers, which will provide oat researchers a useful genomic tool for oat improvement.


Review Publications
Faris, J.D., Zhang, Z., Rasmussen, J.B., Friesen, T.L. 2011. Variable expression of the Stagonospora nodorum effector SnToxA among isolates is correlated with levels of disease susceptibility in wheat. Molecular Plant-Microbe Interactions. 24:1419-1426.

Chu, C.G., Tan, C.T., Zhong, S., Xu, S.S., Yan, L. 2011. A novel retrotransposon inserted in the dominant Vm-B1 allele confers spring growth habit in tetraploid wheat (Triticum turgidum L.). Genes, Genomes, Genetics. 1:637:645.

Lu, S. 2012. Use of the yeast two-hybrid system to identify targets of fungal effectors. In: M. Bolton & B. Thomma (eds), Plant Fungal Pathogens: Methods and Protocols, Methods in Molecular Biology 835:165-189.

Yu, G.T., Wang, T., Anderson, K.M., Harris, M.O., Cai, X., Xu, S.S. 2012. Evaluation and haplotype analysis of elite synthetic hexaploid wheat lines for resistance to Hessian fly. Crop Science. 52:752-763.

Chu, C., Niu, Z., Zhong, S., Chao, S., Friesen, T.L., Halley, S., Elias, E.M., Dong, Y., Faris, J.D., Xu, S.S. 2011. Identification and molecular mapping of two QTLs with major effects for resistance to Fusarium head blight in wheat. Theoretical and Applied Genetics. 123(7):1107-1119.

Munoz-Amatriain, M., Moscou, M.J., Bhat, P.R., Svensson, J.T., Bartos, J., Suchankova, P., Simkova, H., Endo, T.R., Fenton, R.D., Lonardi, S., Castillo, A.M., Chao, S., Cistue, L., Cuesta-Marcos, A., Forrest, K., Hayden, M.J., Hayes, P.M., Horsley, R.D., Moody, D., Sato, K., Valles, M.P., Wulff, B.B., Muehlbauer, G.J., Dolezel, J., Close, T.J. 2011. An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers. The Plant Genome. 4:238-239.

Zhang, Z., Belcram, H., Gornicki, P., Charles, M., Just, J., Huneau, C., Magdelenat, G., Couloux, A., Samain, S., Gill, B.S., Rasmussen, J.B., Barbe, V., Faris, J.D., Chalhoub, B. 2011. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proceedings of the National Academy of Sciences. 108:18737-18742.

Klindworth, D.L., Niu, Z., Chao, S., Friesen, T.L., Jin, Y., Faris, J.D., Cai, X., Xu, S.S. 2012. Introgression and characterization of a goatgrass gene for a high level of resistance to Ug99 stem rust in tetraploid wheat. Genes|Genomes|Genetics. 2:665-673.

Simons, K., Anderson, J.A., Mergoum, M., Faris, J.D., Klindworth, D.L., Xu, S.S., Sneller, C., Ohm, J.-B., Hareland, G.A., Edwards, M.C., Chao, S. 2012. Genetic mapping analysis of bread-making quality traits in spring wheat. Crop Science. 52:2182-2197.

Last Modified: 11/28/2014
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