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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

2010 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.


3.Progress Report
Evaluation of tetraploid wheat accessions for FHB and tan spot resistance. About 150 tetraploid accessions were evaluated at two locations (Fargo and Langdon, ND). A total of 319 tetraploid wheat accessions were evaluated for resistance to tan spot in the greenhouse. Development of synthetic hexaploid wheat lines. A total of 125 synthetic hexaploid wheat lines have been developed by crossing durum, emmer, and Persian wheat collections to Aegilops tauschii. Saturation and fine mapping of H26. A marker close to H26 was used to screen a BAC library. End sequences from positive BACs were used to develop new markers, and comparisons with genomic sequences of related species were conducted. Information from comparative analysis was used to develop additional STS markers. 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 each backcrossed to BR34 as the recurrent parent. The BC2F1 progeny from each of backcrosses were directly evaluated for reactions to respective toxins and BC3F1 progeny for the four genes were produced. Molecular cloning of the Tsn1 gene in wheat. Map-based cloning of the Tsn1 gene was accomplished. The Tsn1 gene was validated by comparative sequence analysis of chemically-induced mutants and wild types, and the full-length transcript of Tsn1 was cloned. Molecular characterization of the Tsn1-ToxA interaction. A wheat cDNA library was constructed and screened for host proteins interacting with Tsn1. Several candidate proteins were identified and their physical interactions with Tsn1 will be further investigated by in vitro co-immunoprecipitation assays. The potential Tsn1-interactors will be tested for possible interactions with ToxA. Characterization of PR-1 genes in wheat. A total of twenty pathogenesis-related protein 1 (PR-1) genes were cloned from hexaploid wheat and their expression patterns and responses to infections of Stagonospora nodorum blotch (SNB) and stem rust pathogens were determined. Thirteen PR-1 genes were mapped. The possible linkage of these PR-1 genes to known disease resistance or other wheat quality-related trait loci will be further investigated. Evaluation of end-use quality traits in hexaploid wheat. A field experiment was conducted to evaluate end-use quality traits in a hard red spring wheat population. The end-use quality traits examined include kernel characteristics, flour and milling yield, dough quality, and bread-baking properties. Molecular-marker based genetic mapping to place genes controlling these characteristics on specific wheat chromosomes is in progress.


4.Accomplishments
1. Identification and characterization of a novel host-toxin interaction in the wheat-Stagonospora nodorum pathosystem. Stagonospora nodorum blotch is a devastating foliar disease of wheat caused by a necrotrophic fungal pathogen, which is known to produce host-selective toxins that are important determinants of disease. ARS scientists in Fargo, ND identified a new toxin produced by S. nodorum and the corresponding wheat gene that confers sensitivity to the toxin. The wheat toxin sensitivity gene, designated Snn4, was mapped to the short arm of chromosome 1A. The toxin, designated SnTox4, was found to be a protein, and compatible Snn4-SnTox4 interactions accounted for more than 40% of the variation in disease development. The identification of SnTox4 and Snn4 provides further support for the notion that the wheat-S. nodorum pathosystem relies on host recognition of pathogen-produced toxins for disease development, and this system can serve as a model for other host-necrotrophic pathogen systems.

2. Genetic analysis of disease susceptibility caused by compatible Tsn1-SnToxA and Snn1-SnTox1 interactions in the wheat-Stagonospora nodorum pathosystem. The necrotrophic fungus Stagonospora nodorum produces numerous host-selective toxins, including SnToxA and SnTox1, to cause a foliar disease of wheat known as Stagonospora nodorum blotch. The wheat genes Tsn1 and Snn1 confer sensitivity to SnToxA and SnTox1, respectively. ARS scientists in Fargo, ND compared the effects of compatible Tsn1-SnToxA and Snn1-SnTox1 on disease and found that they are completely additive. This result provides knowledge regarding pathogen virulence effectors, and suggests that wheat breeders and geneticists need to remove all toxin sensitivity genes from adapted germplasms to obtain complete resistance.

3. Genotyping of wheat and barley lines for marker-assisted breeding projects. The small grains genotyping laboratory at Fargo is equipped for high-throughput genotyping, which can greatly accelerate the development of superior wheat and barley varieties. ARS scientists in Fargo, ND used high-throughput genotyping technologies to screen more than 10,000 wheat breeding lines and 5,000 barley breeding lines adapted to the Northern Plains region with DNA markers associated with Fusarium head blight resistance, rust resistance (leaf and stem), high grain protein content, tan spot resistance, bread-making quality, and photoperiod in wheat; and Fusarium head blight resistance and net blotch resistance in barley. The genotyping data were used by breeders to select lines as parents to initiate breeding cycles, and to select elite lines for advanced yield trials.

4. Identification of single nucleotide variations associated with disease resistances in barley. Single nucleotide polymorphisms are highly abundant in plant genomes and a large number of single nucleotide polymorphism markers have been developed in barley. Using a high throughput genotyping system, ARS scientists in Fargo, ND evaluated genetic variations based on single nucleotide differences at over 3,000 chromosomal locations present in the genomes of more than 1,000 barley breeding lines and germplasm, and provided several million data points to breeders and geneticists. After mining these data using statistical tools, we identified the single nucleotide variations associated with genes influencing Fusarium head blight disease and mycotoxin resistance, as well as spot blotch resistance in barley. The information regarding single nucleotide polymorphisms will be used to develop useful DNA marker resources to facilitate breeding cultivars with improved disease resistance, and thus minimize yield and quality reduction of barley in the Upper Midwest region.

5. Development of a tetraploid wheat mapping population and molecular marker-based linkage maps. Much effort has been placed in constructing molecular marker-based genetic maps in hexaploid (bread) wheat, but little has been done to develop molecular maps in durum wheat. To facilitate genetic and genomic studies of durum wheat, ARS scientists in Fargo, ND developed a tetraploid wheat doubled haploid (DH) population comprised of 146 lines derived from a cross between the durum cultivar ‘Lebsock’ and the Persian wheat accession PI 94749. The DH population was then used to construct genetic maps of all 14 chromosomes with 280 molecular markers. The DH population and genetic maps developed in this study will be useful for genetic dissection of important agronomic traits as well as the identification and development of markers for marker-assisted selection. Five genes controlling resistance to two races of the tan spot fungus were identified using the DH population and the genetic maps.

6. Characterization of durum wheat single chromosome substitution lines. The durum wheat cultivar ‘Golden Ball’ (GB) is a source of resistance to wheat sawfly due to its superior solid stem. A complete set of 14 ‘Langdon’ (LDN)-GB disomic substitution (DS) lines were previously developed by using GB as the chromosome donor and LDN as the recipient. ARS scientists in Fargo, ND used molecular marker analysis to show that the 14 substitution lines all have correct chromosome assignments, but they have genetic backgrounds that are not highly consistent with their recipient parent LDN. Evaluation of stem-solidness in the substitution lines indicated that chromosome 3B controls stem solidness in GB. This research provides useful information for the utilization of GB and LDN-GB DS lines for genetic and genomic studies of tetraploid wheat and for the improvement of sawfly resistance in durum and bread wheat.


Review Publications
Xu, S.S., Jin, Y., Klindworth, D.L., Wang, R., Cai, X. 2009. Evaluation and Characterization of Seedling Resistances to Stem Rust Ug99 Races in Wheat-Alien Species Derivatives. Crop Science. 49:2167–2175.

Abeysekara, N., Friesen, T.L., Keller, B., Faris, J.D. 2009. Identification and Characterization of a Novel Host-Toxin Interaction in the Wheat - Stagonospora Nodorum Pathosystem. Theoretical and Applied Genetics. 120:117-126

Close, T.J., Bhat, P., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J., Wanamaker, S., Bozdag, S., Roose, M., Moscou, M., Chao, S., Varshney, R., Szucs, P., Sato, K., Hayes, P., Matthews, D.E., Kleinhofs, A., Muehlbauer, G., Deyoung, J., Marshall, D.F., Madishetty, K., Fenton, R.D., Condamine, P., Graner, A., Waugh, R. 2009. Development and Implementation of High-Throughput SNP Genotyping in Barley. Biomed Central (BMC) Genomics. 10:582.

Chu, C., Chao, S., Friesen, T.L., Faris, J.D., Zhong, S., Xu, S.S. 2009.Novel Tan Spot Resistance QTLs Detected Using an SSR-Based Linkage Map of Tetraploid Wheat. Molecular Breeding. 25:327-338.

Hamblin, M.T., Close, T.J., Bhat, P.R., Chao, S., Abraham, K., Blake, T., Brooks, W.S., Cooper, B., Griffey, C.A., Hayes, P.M., Hole, D.J., Horsley, R.D., Obert, D.E., Smith, K.P., Ullrich, S.E., Muehlbauer, G.J., Jannink, J. 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Science. 50:556-566.

Xu, S.S., Chu, C.G., Chao, S., Klindworth, D.L., Faris, J.D., Elias, E.M. 2010. Marker-assisted Characterization of Durum Wheat Langdon-Golden Ball Disomic Substitution Lines. Theoretical and Applied Genetics.120:1575-1585

Faris, J.D., Friesen, T.L. 2009. Re-Evaluation of a Tetraploid Wheat Population Indicates That the Tsn1-ToxA Interaction is the Only Factor Governing Stagonospora Nodorum Blotch Susceptibility. Phytopathology. 99:(8) 906-912

Friesen, T.L., Chu, C.G., Liu, Z.H., Xu, S.S., Halley, S., Faris, J.D. 2009. Host-selective toxins produced by Stagonospora nodorum confer disease susceptibility in adult wheat plants under field conditions. Theoretical and Applied Genetics. 118:1489-1497

Cai, X., Xu, S.S., Zhu, X. 2010. Ploidy-Dependent Unreductional Meiotic Cell Division in Polyploid Wheat. Chromosoma. 119:275-285

Yu, G., Zhang, Q., Klindworth, D.L., Friesen, T.L., Knox, R., Jin, Y., Zhong, S., Cai, X., Xu, S.S. 2010. Molecular and Cytogenetic Characterization of Aegilops Speltoides Chromosome Segments Carrying Sr39 in the Original Translocation Stock and Derived Wheat Lines. Crop Science. 50:1393–1400.

Feng, J., Primomo, V., Zhang, Y., Jan, C., Tulsieram, L., Xu, S.S. 2009. Physical Localization and Genetic Mapping of Fertility Restoration Gene Rfo in Canola (Brassica napus L.). Genome. 52:401-407

Gu, X., Zhang, L., Glover, K., Chu, C., Xu, S.S., Faris, J.D., Friesen, T.L., Ibrahim, A. 2010. Genetic Variation of Seed Dormancy in Synthetic Hexaploid Wheat-Derived Populations. Crop Science. 50:1318-1324.

Chao, S., Xu, S.S., Elias, E., Faris, J.D., Sorrells, M. 2010. Identification of Chromosome Locations of Genes Affecting pre-Harvest Sprouting and Seed Dormancy using Chromosome Substitution Lines in Tetraploid Wheat (Triticum turgidum L.). Crop Science. 50:1180-1187

Yu, G., Williams, C.E., Harris, M.O., Cai, X., Mergoum, M., Xu, S.S. 2010. Development and Validation of Molecular Markers Closely LinKed to H32 for Resistance to Hessian Fly in Wheat. Crop Science. 50:1325-1332.

Last Modified: 9/10/2014
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