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United States Department of Agriculture

Agricultural Research Service


Location: Cereal Crops Research

2009 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 accessions for Fusarium head blight resistance in the greenhouse and synthetic hexaploid lines for Hessian fly resistance: A total of 577 tetraploid wheat accessions were tested for Fusarium head blight resistance. One hundred and twenty synthetic hexaploid wheat lines along with their durum parents were evaluated for resistance to the Hessian fly. 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 BC1F1 progeny from each of backcrosses were directly evaluated for reactions to respective toxins. Development of synthetic hexaploid wheat lines: About 80 tetraploid wheat accessions were initially crossed with Aegilops tauschii and 20 new SHW lines have been developed. Saturation mapping of H26: A large F2 population from Aegilops tauschii was evaluated for resistance to Hessian fly and approximately 3,000 susceptible homozygous plants have been identified and were used for fine mapping of H26. To date, two STS markers have been identified at 0.1 cM from the H26 locus. Introgression of tan spot and Stagonospora nodorum blotch resistance genes into adapted durum and hard red spring wheat germplasm: The recombinant inbred line BG214 with genes for resistance was crossed with Glenn and Divide. A large number of BC1F1 progeny have been developed by backcrossing F1 plants to Glenn and Divide. The identification of quantitative trait loci associated with bread making quality in a hard red spring wheat population: A recombinant inbred population was planted in the field at multiple locations. Plants harvested from three locations were evaluated for quality traits. Genotyping of wheat and barley lines for marker-assisted breeding projects: The genotyping lab continues to collaborate with durum wheat, spring wheat and barley breeders in the Northern Plains region to screen breeding lines using DNA markers linked to targeted agronomic traits. The identification of SnToxA interactors: A wheat cDNA library was constructed and screened for proteins interacting with SnToxA. Two pathogenesis-related proteins have been confirmed to physically bind to SnToxA and are likely regulated by Tsn1, the major disease susceptibility gene in wheat. The characterization of PR-1 genes in wheat: A total of eighteen pathogenesis-related protein 1 (PR-1) genes have been cloned from hexaploid wheat and their expression patterns upon infection by Stagonospora nodorum have been determined. Genomic mapping are underway to investigate the possible linkage of these PR-1 genes to known disease resistance trait loci in wheat. Introgression of Fusarium head blight resistance from wild emmer wheat into durum wheat: Tetraploid wheat lines homozygous for the Fusarium head blight resistance loci on chromosomes 3A and 6B were identified with molecular markers. These lines were crossed to a line that has a Fusarium head blight resistance locus on chromosome 7A. The resulting F1 plant was crossed to the durum variety Divide.

4. Accomplishments
1. Identification of novel tan spot resistance genes in wheat. Tan spot 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 evaluated tan spot resistance in a segregating wheat population derived from a synthetic hexaploid wheat and a hard red spring wheat breeding line. Using quantitative trait loci analysis to identify chromosomal regions associated with tan spot resistance, novel tan spot resistance loci that were not associated with previously identified toxin sensitivity loci were identified. Some of the quantitative trait loci conferred race nonspecific resistance suggesting they were not due to toxin sensitivity genes. These quantitative trait loci and the molecular markers associated with them will be useful for the development of tan spot resistant wheat germplasm and varieties that harbor broad spectrum and durable tan spot resistance.

2. Genomic analysis of the Snn1 locus. The necrotrophic fungus Stagonospora nodorum causes a foliar disease of wheat known as Stagonospora nodorum blotch. S. nodorum is known to produce a large number of host selective toxins that are important determinants of disease. The wheat Snn1 gene confers sensitivity to the S. nodorum host-selective toxin designated SnTox1. Molecular markers were used to develop a detailed map of the genomic region containing Snn1 and to conduct comparative mapping analysis with a similar region in the rice genome. This led to the development of markers tightly flanking the Snn1 gene, which will be useful in marker-assisted breeding programs to eliminate the Snn1-conferred toxin sensitivity, and therefore lead to Stagonospora nodorum blotch resistant wheat germplasm and cultivars.

3. Identification, development, and validation of marker-assisted selection against the Stagonospora nodorum toxin sensitivity genes Tsn1 and Snn2 in wheat. The wheat foliar pathogen Stagonospora nodorum produces numerous host selective toxins, including SnToxA and SnTox2, that are important virulence factors. The wheat genes Tsn1 and Snn2 confer sensitivity to SnToxA and SnTox2, respectively, and are therefore considered as factors for disease susceptibility. ARS scientists in Fargo, ND developed molecular markers that tightly flank Tsn1 and Snn2. The evaluation of a large and diverse set of wheat accessions with the markers and for reaction to SnToxA and SnTox2 indicated that the markers are highly diagnostic for reaction to the toxins. Therefore, these markers will be very useful to wheat geneticists and breeders who wish to eliminate S. nodorum toxin sensitivity and develop resistant germplasm and varieties.

4. Evaluation of host-selective toxins produced by Stagonospora nodorum in conferring disease susceptibility in adult wheat plants under field conditions. The wheat foliar pathogen Stagonospora nodorum produces numerous host selective toxins, including SnToxA and SnTox2, that are known to be important determinants of disease in juvenile plants. However, it has not been shown whether these toxins are important for disease development in adult plants. ARS scientists in Fargo, ND evaluated a segregating wheat population in multiple years and field locations for reaction to disease caused by S. nodorum, and conducted quantitative trait loci analysis to determine if the toxins were associated with disease development. The results indicated that Tsn1 and Snn2, the wheat genes that confer sensitivity to SnToxA and SnTox2, were significantly associated with disease and explained 18 and 15 percent of the variation, respectively. Therefore, S. nodorum toxins are associated with disease in juvenile as well as adult plants and the elimination of Tsn1 and Snn2 from wheat germplasm and varieties would result in higher levels of resistance to S. nodorum.

5. 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 excel the development of superior wheat and barley varieties. ARS scientists in Fargo, ND continued to collaborate with three spring wheat, two durum wheat and two barley breeding projects in the Northern Plains region on marker-assisted selection projects with a focus on screening and selecting breeding lines using markers associated with Fusarium head blight resistance, leaf rust resistance, high grain protein content, tan spot resistance, Stagonospora nodorum resistance, and favorable alleles for bread making quality at loci encoding high molecular weight glutenins in wheat; and Fusarium head blight resistance and net blotch resistance in barley. In addition, collaboration with a breeding program at the University of Minnesota led to the development of a diagnostic marker for a stem rust resistance gene that can be used for gene pyramiding and marker-assisted selection.

6. Analysis of single nucleotide polymorphism markers in wheat and barley using the Illumina genotyping platform. Single nucleotide polymorphisms are highly abundant in plant genomes and a large number of single nucleotide polymorphism markers have been developed in both wheat and barley. As part of a barley coordinated agricultural project, 3072 single nucleotide polymorphism markers were genotyped on a total 1,920 breeding lines acquired from ten U.S. barley breeding programs. Approximately 6-million data points were made available to breeders and geneticists. These data are being evaluated for association genetics studies in barley. The suitability of using the Illumina platform in polyploid species was also investigated. In collaboration with a scientist at Kansas State University, 1536 gene-derived single nucleotide polymorphism markers were developed and used to genotype 576 wheat breeding lines contributed from wheat breeders in the U.S., CIMMYT and Australia. The high quality data has encouraged a collaborative effort on developing large scale single nucleotide polymorphism markers and the use of Illumina platform to generate data for association genetics studies in wheat.

7. Characterization of durum Langdon – wild emmer wheat chromosome substitution lines for agronomic traits. Wild emmer wheat has been a useful source of genes for desirable agronomic and quality traits in wheat. Two sets of durum chromosome substitution lines in which specific chromosomes from wild emmer accessions replace a chromosome from durum wheat cultivar Langdon are useful tools for the identification of important agronomic genes on individual wild emmer chromosomes. Twenty-three substitution lines from the two sets were grown in replicated yield trials at two locations in North Dakota for two years. Potentially useful variation for grain protein content, thousand-kernel-weight, kernel size, semolina extraction, and semolina brightness and color, was identified. Eight lines had significantly higher grain protein content than Langdon, and will be potentially useful for improving grain protein content in durum wheat varieties.

8. Identification and characterization of new source of Ug99 stem rust resistance derived from wild relative species of wheat. Stem rust, a devastating disease of wheat, has been effectively controlled worldwide for the past 50 years by deployment of stem rust resistance genes in wheat cultivars. However, a new race of stem rust known as Ug99 recently emerged in eastern Africa, and this race overcomes most of the stem rust resistance genes currently deployed in wheat cultivars worldwide. To identify new sources of stem rust resistance genes that are effective against Ug99, we evaluated 65 wheat lines derived from crosses of bread wheat or durum wheat with eight wild relative species, including two goatgrass species and six perennial wheatgrass species. The result showed that 34 wheat-alien species derivatives had resistance to Ug99 and suggest that several lines carry novel genes for stem rust resistance. The wheat-wild relative derivatives are an important germplasm base for stem rust resistance, and they should be useful for introducing novel stem rust resistance genes into wheat breeding.

Review Publications
Faris, J.D., Xu, S.S., Xiwen, C., Friesen, T.L., Jin, Y. 2008. Molecular and cytogenetic characterization of a durum wheat Aegilops speltoides chromosome translocation conferring resistance to stem rust. Chromosome Research. 16(8): 1097-1105.

Anderson, J.A., Chao, S., Liu, S. 2008. Molecular Breeding Using a Major QTL for Fusarium Head Blight Resistance in Wheat. Crop Science. 47(3):S112-S119

Liu, S., Chao, S., Anderson, J.A. 2008. New DNA Markers for High Molecular Weight Glutenin Subunits in Wheat. Theoretical and Applied Genetics. 118:177-183

Zhang, W., Chao, S., Manthey, F., Chicaiza, O., Brevis, J.C., Echenique, J., Dubcovsky, J. 2008. Qtl analysis of pasta quality using a composite microsatellite - snp map of durum wheat. Theoretical and Applied Genetics. 117:1361-1377

Tsilo, T., Chao, S., Jin, Y., Anderson, J. 2009. Identification and validation of SSR markers linked to the stem rust resistance gene Sr6 on the short arm of chromosome 2D in wheat. Theoretical and Applied Genetics. 118:515-524

Szucs, P., Blake, V.C., Chao, S., Marcos-Cuesta, A., Muehlbauer, G.J., Ramsay, L., Waugh, R., Hayes, P.M. 2009. An integrated resource for barley linkage map and malting quality QTL alignment. The Plant Genome. 2(2):134-140, 2009

Mergoum, M., Singh, P.K., Anderson, J.A., Pena, R.J., Singh, R.P., Xu, S.S., Ransom, J.K. 2009. Spring Wheat Breeding. Book Chapter. Century. P.127-156. In: M.J. Carena (ed.) Handbook of Plant Breeding Vol. 3. Cereals. Springer, New York

Chalupska, D., Lee, H.Y., Faris, J.D., Evrard, A., Chalhoub, B., Haselkorn, R., Gornicki, P. 2008. Acc homoeoloci and the evolution of wheat genomes. Proceedings of the National Academy of Sciences. 105:9691-9696

Klindworth, D.L., Hareland, G.A., Elias, E.M., Faris, J.D., Chao, S., Xu, S.S. 2009. Agronomic and Quality Characteristics of Two New Sets of Langdon Durum – wWld Emmer Wheat Chromosome Substitution Lines. Journal of Cereal Science 50: 29-35

Jannink, J., Iwata, H., Bhat, P.R., Chao, S., Wenzl, P., Muehlbauer, G.J. 2009. Marker imputation in barley association studies. The Plant Genome. 2:11-22.

Yu, G., Cai, X., Harris, M., Gu, Y.Q., Luo, M., Xu, S.S. 2009. Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat. Theoretical and Applied Genetics. 118(8):1589-1599.

Last Modified: 05/23/2017
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