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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Research Project #424595

Research Project: Genetic Improvement of Durum and Spring Wheat for Quality and Resistance to Diseases and Pests

Location: Cereal Crops Research

2015 Annual Report

The proposed research involves the use of genetics and genomics to gain understanding of the genes associated with mechanisms of disease resistance or susceptibility and end use quality, and the identification, characterization, and development of genetic stocks, germplasm, and tools for the improvement of wheat and other small grains. Specific objectives are: 1. Identify new genes and sources for resistance and end-use quality in wheat. 1A. Identify new sources of Hessian fly resistance among wheat wild relatives of the Aegilops genus and newly developed synthetic hexaploid wheats. 1B. Identify new sources of stem rust resistance among wheat relatives of the Thinopyrum genus and newly developed synthetic hexaploid wheats. 1C. Identify new sources of Fusarium head blight (FHB), tan spot, and Stagonospora nodorum blotch (SNB) resistance among newly developed synthetic hexaploid wheats. 1D. Identify novel genes for resistance to stem rust, tan spot, SNB, and Hessian fly among the National Small Grains Collection and a collection of domesticated emmer accessions using association mapping. 1E. Identify novel genes for end-use quality among entries of the Uniform Regional Nursery using association mapping. 2. Identify and develop molecular markers for rusts, necrotrophic diseases, and pre-harvest sprouting in wheat. 2A. Determine the chromosomal locations of novel genes conferring sensitivity to newly identified host-selective toxins produced by S. nodorum using molecular markers. 2B. Develop molecular markers suitable for MAS of the S. nodorum toxin sensitivity genes Snn3-B1 and Snn3-D1 through genomic analysis and fine-mapping. 2C. Determine the chromosomal location of a new Ug99 stem rust resistance gene using molecular markers. 2D. Develop markers and populations for the fine-mapping and initiation of the map-based cloning of the Ug99 stem rust resistance gene Sr47. 2E. Develop molecular markers suitable for MAS of pre-harvest sprouting resistance QTLs on chromosome 2B in tetraploid wheat. 3. Characterize the genetic mechanisms of resistance involved in wheat-necrotrophic pathogen interactions. 3A. Determine the structural and functional diversity of the Tsn1 gene among accessions of the wild wheat ancestor Aegilops speltoides. 3B. Identify genes and/or genetic mechanisms involved in the Tsn1-ToxA interaction. 3C. Characterize the structure and function of families of Pr-1 and Pr-2 genes in wheat. 4. Develop genetic resources and tools for the improvement of wheat and other small grains. 4A. Develop HRSW lines nearly isogenic for S. nodorum toxin sensitivity genes. 4B. Develop adapted solid-stem durum wheat germplasm for resistance to sawfly. 4C. Develop durum and wheat germplasm with FHB and stem rust resistance. 4D. Develop a reference SNP map for durum wheat. 4E. Develop a SNP marker set for MAS in wheat. 4F. Provide genotyping services for barley, wheat, and oat varietal development.

Durum and hard red spring wheat (HRSW) varieties with improved end-use quality and resistance to abiotic and biotic stresses are needed to meet the nutritional demands of the world’s growing population. This challenge must be met through the discovery and deployment of genes for disease resistance and traits that effect quality such as kernel texture, protein content, flour yield, dough strength, and baking performance. In this project, we will identify new sources of resistance to diseases and pests, and improved quality. Molecular mapping populations will be generated and used to identify genes and quantitative trait loci governing resistance to Stagonospora nodorum blotch, stem rust, and pre-harvest sprouting. This work will yield knowledge of the genetic mechanisms controlling these traits, the development of markers for marker-assisted selection, and genetic stocks and germplasm useful forgene deployment. Additional work on the molecular characterization of the genes and genetic pathways associated with wheat-necrotrophic pathogen interactions will be conducted as part of this project and will yield basic knowledge useful for devising novel strategies for developing crops with resistance to necrotrophic pathogens. Finally, genetic resources and tools for the development of improved wheat and durum cultivars will be generated, including stocks for the genetic analyses of Stagonospora nodorum blotch susceptibility genes, adapted germplasm with resistance to sawfly, Fusarium head blight, and stem rust, and high-throughput molecular marker sets for genomic selection in durum and common wheat. In addition, genotyping services will be provided to regional wheat, durum, barley, and oat breeders to expedite the development of improved varieties.

Progress Report
Identification of new sources of Hessian fly resistance in Aegilops species. A total of 492 accessions belonging to many different species of the Aegilops genus (a wild relative of modern wheat) were evaluated for resistance to the Great Plains (GP) biotype of Hessian fly. This work relates directly to objective 1. Identification of novel genes for resistance to multiple wheat diseases in primitive wheat. A panel of 180 cultivated emmer wheat accessions deposited at the USDA-ARS National Small Grains Collection, Aberdeen, ID, was evaluated for resistance to the diseases stem rust, tan spot, SNB, and Hessian fly in greenhouse experiments. The data from disease evaluation experiments and marker analysis are currently being used to identify novel genes associated with resistance. This work relates directly to objective 1. Identification of a new gene governing susceptibility to Septoria nodorum blotch in wheat. The screening of genetic stocks involving individual chromosome substitutions for reaction to the disease Septoria nodorum blotch revealed that chromosome 2D from the wheat line Thatcher harbored a novel susceptibility gene. The gene, designated Snn7, was mapped to the long arm of chromosome 2D using molecular markers. When the pathogen produced protein designated SnTox7 was recognized by Snn7, there was a compatible interaction and disease ensued. This work relates directly to objective 3. Development of molecular markers associated with the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Saturation, comparative, and high-resolution mapping were conducted to develop and identify molecular markers tightly linked to the Snn3-B1 gene on chromosome arm 5BS in wheat. User-friendly PCR-based markers delineating the gene to a small interval were developed and will be useful for isolating the Snn3-B1 DNA sequence and also for breeders who wish to use marker-assisted selection to remove the Snn3-B1 susceptibility gene from their germplasm to develop disease-resistant lines. This work relates directly to objective 3. Identification of a form of the wheat Tsn1 gene in maize. Research revealed that corn contains a gene similar to the wheat Tsn1 gene, which acts to make wheat susceptible to certain fungal pathogens. Molecular analysis of the maize Tsn1-like gene confirmed that it belongs to the same family as the wheat Tsn1 gene. Further studies may help the understanding of the molecular basis of Tsn1-regulated disease susceptibility in wheat and possibly corn as well. This work relates directly to objective 3. Development of hard red spring wheat lines that are genetically identical except for single genes that govern susceptibility to the disease Septoria nodorum blotch (SNB). Multiple cross hybridizations between three lines that each carry a single SNB susceptibility gene and the line BR34, which carries no SNB susceptibility genes, were made with the goal of developing three lines that are identical (isogenic) with the exception of the single SNB susceptibility genes. These lines will be useful for conducting genetic analyses of SNB resistance/susceptibility. This work relates directly to objective 4. Development of adapted solid-stem durum wheat germplasm for resistance to sawfly. The Durum wheat cultivar Golden Ball with solid stem was previously crossed with the North Dakota durum cultivar 'Divide' and the F1 hybrid was backcrossed with Divide and two other North Dakota durum cultivars 'Albabo' and 'Grenora'. Two more backcrosses were made using the three durum cultivars as the recurrent parents to introgress the solid stem trait into Divide, Albabo, and Grenora. This work relates directly to objective 4. Development of durum and bread wheat germplasm with stem rust resistance. Multiple cross hybridizations were performed to move the stem rust resistance genes Sr39 and Sr47 into multiple modern durum and bread wheat varieties. This work relates directly to objective 4.

1. Identification of a gene for fungal disease resistance in wheat. Septoria 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 used genetic analyses to compare resistant and susceptible wheat lines and found a single gene associated with the development of SNB. The results indicated that the gene was present in the susceptible wheat line and actually caused susceptibility to the disease through recognition of a specific protein produced by the pathogen, whereas the lack of this recognition in the other lines resulted in a resistant response. The molecular markers found to be associated with the susceptibility gene will be useful for wheat breeders to efficiently remove it from breeding lines.

2. Identification of genes governing domestication and agronomic performance in durum wheat. Genetic improvements in durum wheat are needed to increase production and to meet demands for human consumption. Knowledge of genes and genetic transitions in durum wheat progenitors that govern domestication and other desirable traits is useful for improvement of modern durum varieties. ARS researchers in Fargo, ND conducted genetic analysis of a primitive form of durum wheat known as cultivated emmer and identified several genes that underwent mutation to give rise to fully domesticated durum wheat. Further analysis also revealed that the cultivated emmer harbored genes that, when combined with certain genes that currently exist in domesticated durum wheat, will enhance yield and productivity. This work shed light on the events that shaped durum domestication and it also showed that cultivated emmer wheat can be a useful source of genes for durum variety improvement.

3. Identification of a stem rust resistance gene in wheat. The stem rust resistance gene Sr46, an effective gene against the highly virulent African strain Ug99, was previously identified in an accession of goatgrass (a close relative of domesticated wheat) in Australia. However, this gene's chromosomal location had not been determined. ARS researchers in Fargo, ND, identified a different goatgrass line and modern wheat derivatives that carry Sr46. Genetic research using DNA markers revealed the chromosomal location of the gene. The wheat lines carrying Sr46 and the DNA markers identified in this research to be closely associated with the gene provide useful resources for the development of stem rust resistant wheat varieties.

4. A fungal protein responsible for causing disease in wheat also found in a corn pathogen. A protein known as ToxA is produced by two fungal pathogens of wheat and is known to be a primary culprit in causing disease, but how it works and where it came from are still a mystery. ARS researchers in Fargo, ND used molecular techniques to identify a protein with strong similarity to ToxA in a fungal pathogen of corn, and they showed that the ToxA from the corn pathogen plays a role in causing disease similar to that of the ToxA from the wheat pathogens. They also found that ToxA-like proteins actually exist in other plant-pathogenic fungi as well. These results suggest that ToxA-like proteins may have a common ancestor in fungi and that the proteins attack wheat, corn, and other cereals in similar ways to cause disease.

5. Identification of scab resistance genes in emmer and durum wheat. Fusarium head blight (FHB), commonly known as scab, presently threatens durum wheat production in the Unites States and many other durum-growing regions. Because durum wheat lacks high levels of FHB resistance, it is crucial to identify FHB resistance sources for durum wheat breeding programs. ARS researchers in Fargo, ND, in cooperation with North Dakota State University scientists, identified a cultivated emmer wheat line (a close relative of modern durum wheat) with a moderate level of FHB resistance. Genetic analysis of the emmer wheat line and a modern durum variety led to the identification of two FHB resistance genes in the emmer line and one in the durum variety. This study indicates that combining FHB resistance genes from emmer wheat with the resistance genes from durum varieties will be useful for improving FHB resistance in durum wheat.

6. Identification of genes affecting pre-harvest sprouting tolerance (PHS) in durum wheat. PHS is germination of grain in the ear under wet field conditions prior to harvesting. PHS damage often leads to a reduction in both grain yield and grain quality. Identification of resources with better PHS tolerance will be beneficial for improving PHS tolerance in durum wheat. ARS researchers in Fargo, ND and their collaborators at North Dakota State University and Cornell University used genetic analysis to identify genes affecting PHS tolerance originated from wild emmer, a close relative of cultivated durum wheat. Wheat lines carrying the genes tended to have higher seed dormancy levels, and thus better PHS tolerance, than those without them. The resources identified in this study should be useful for breeding durum wheat cultivars with higher PHS tolerance.

Review Publications
Zheng, Q., Klindworth, D.L., Friesen, T.L., Liu, A., Li, Z., Zhong, S., Jin, Y., Xu, S.S. 2014. Characterization of Thinopyrum species for wheat stem rust resistance and ploidy level. Crop Science. 54:2663-2672.
Maccaferri, M., Cane, M.A., Sanguineti, M.C., Salvi, S., Colalongo, M.C., Massi, A., Clarke, F., Knox, R., Pozniak, C.J., Clarke, J.M., Fahima, T., Dubcovsky, J., Xu, S., Ammar, K., Karsai, I., Vida, G., Tuberosa, R. 2014. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. BMC Genomics. 15:873.
Yu, G., Zhang, Q., Friesen, T.L., Rouse, M.N., Jin, Y., Zhong, S., Rasmussen, J.B., Lagudah, E.S., Xu, S.S. 2015. Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen. Theoretical and Applied Genetics. 128:431-443.
Zhang, Q., Axtman, J.E., Faris, J.D., Chao, S., Zhang, Z., Friesen, T.L., Zhong, S., Cai, X., Elias, E.M., Xu, S.S. 2014. Identification and molecular mapping of quantitative trait loci for Fusarium head blight resistance in emmer and durum wheat using a single nucleotide polymorphism-based linkage map. Molecular Breeding. 34:1677-1687.
Maccaferri, M., Ricci, A., Salvi, S., Milner, S.G., Noli, E., Martelli, P.L., Casadio, R., Akhunov, E., Scalabrin, S., Vendramin, V., Ammar, K., Blanco, A., Desiderio, F., Distelfeld, A., Dubcovsky, J., Fahima, T., Faris, J.D., Korol, A., Massi, A., Mastrangelo, A.M., Morgante, M., Pozniak, C., N'Diaye, A., Xu, S., Tuberosa, R. 2015. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal. 13:648-663.
Macaferri, M., Zhang, J., Bulli, P., Abate, Z., Chao, S., Cantu, D., Bossolini, E., Chen, X., Pumphrey, M., Dubcovsky, J. 2015. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). Genes, Genomes, and Genomics. 5(3):449-465.
Mohammadi, M., Blake, T.K., Budde, A.D., Chao, S., Hayes, P.M., Horsley, R.D., Obert, D.E., Ullrich, S.E., Smith, K.P. 2015. A genome-wide association study of malting quality across eight U.S. barley breeding programs. Theoretical and Applied Genetics. 128:705-721.
Bonman, J.M., Babiker, E.M., Cuesta-Marcos, A., Esvelt Klos, K.L., Brown Guedira, G.L., Chao, S., See, D.R., Chen, J., Akhunov, E., Zhang, J., Bockelman, H.E., Gordon, T.C. 2015. Genetic diversity among wheat accessions from the USDA National Small Grains Collection. Crop Science. 55(3):1243-1253.
Goodwin, S.B., Cavaletto, J.R., Hale, I.L., Thompson, I.A., Xu, S.S., Adhikari, T.B., Dubcovsky, J. 2015. A new map location of Gene Stb3 for resistance to Septoria Tritici Blotch in wheat. Crop Science. 55:35-43.
Harris, M.O., Friesen, T.L., Xu, S.S., Chen, M.S., Giron, D., Stuart, J.J. 2015. Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress. Journal of Experimental Botany. 66(2):513-531.
Liu, Z., Holmes, D.J., Faris, J.D., Chao, S., Brueggeman, R., Edwards, M.C., Friesen, T.L. 2015. Necrotrophic effector-triggered susceptibility (NETS) underlies the barley-Pyrenophora teres f. teres interaction specific to chromosome 6H. Molecular Plant Pathology. 16(2):188-200.
Eckard, J., Gonzales-Hernandez, J., Chao, S., St Amand, P., Bai, G. 2014. Construction of dense linkage maps "on the fly" using early generation wheat breeding populations. Molecular Breeding. DOI:10.1007/s11032-014-0116-1.
Faris, J.D., Zhang, Q., Chao, S., Zhang, Z., Xu, S.S. 2014. Analysis of agronomic and domestication traits in a durum x cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map. Theoretical and Applied Genetics. 127:2333-2348.
Islamovic, E., Obert, D., Budde, A.D., Schmitt, M., Brunick II, R., Kilian, A., Chao, S., Lazo, G.R., Marshall, J., Jellen, E., Maughan, P., Hu, G., Esvelt Klos, K.L., Brown, R., Jackson, E. 2014. Quantitative trait loci of barley malting quality trait components in the Stellar/01Ab8219 mapping population. Molecular Breeding. DOI: 10.1007/s11032-014-0017-3.
Lu, S., Faris, J.D., Sherwood, R., Friesen, T.L., Edwards, M.C. 2014. A dimeric PR-1-type pathogenesis-related protein interacts with ToxA and potentially mediates ToxA-induced necrosis in sensitive wheat. Molecular Plant Pathology. 15(7):650-663.
Mohammadi, M., Endelman, J.B., Nair, S., Chao, S., Jones, S.S., Muehlbauer, G.J., Ullrich, S.E., Baik, B.-K., Wise, M.L., Smith, K.P. 2014. Association mapping of grain hardness, polyphenol oxidase, total phenolics, amylose content, and ß-glucan in US barley breeding germplasm. Molecular Breeding. 34:1229-1243.
Oliver, R.E., Islamovic, E., Obert, D.E., Wise, M.L., Herrin, L.L., Hang, A., Harrison, S.A., Ibrahim, A., Marshall, J.M., Miclaus, K.J., Lazo, G.R., Chao, S., Hu, G., Jackson, E. 2014. Comparative systems biology reveals allelic variation modulating tocochromanol profiles in barley. PLoS One. 9:e96276.
Rouse, M.N., Nirmala, J.H., Jin, Y., Chao, S., Fetch, T.G., Pretorius, Z., Hiebert, C. 2014. Characterization of Sr9h, a Ug99-resistant allele of wheat stem rust resistance gene Sr9, and coupling to Sr28 on chromosome arm 2BL. Journal of Theoretical and Applied Genetics. 127:1681-1688.
Shjerve, R.A., Faris, J.D., Brueggeman, R.S., Yan, C., Zhu, Y., Koladia, V., Friesen, T.L. 2014. Evaluation of a Pyrenophora teres f. teres mapping population reveals multiple independent interactions with a region of barley chromosome 6H. Fungal Genetics and Biology. 70:104-112.
Tinker, N.A., Chao, S., Lazo, G.R., Oliver, R.E., Huang, Y.-F., Poland, J.A., Jellen, E.N., Maughan, P.J., Kilian, A., Jackson, E.W. 2014. A SNP genotyping array for hexaploid oat. The Plant Genome. 7(3). doi: 10.3835/plantgenome2014.03.0010
Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B.E., Maccaferri, M., Salvi, S., Milner, S.G., Cattivelli, L., Mastrangelo, A.M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., International Wheat Genome Sequencing Consortium, Lillemo, M., Mather, D., Appels, R., Dulferos, R., Brown-Guedira, G., Korol, A., Akhunova, A.R., Feuillet, C., Salse, J., Morgante, M., Pozniak, C., Luo, M.-C., Dvorak, J., Morell, M., Dubcovsky, J., Ganal, M., Tuberosa, R., Lawley, C., Mikoulitch, I., Cavanagh, C., Edwards, K.J., Hayden, M., Akhunov, E. 2014. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal. 12:787-796.
Zheng, Q., Lv, Z., Niu, Z., Li, B., Li, H., Xu, S.S., Han, F., Li, Z. 2014. Molecular cytogenetic characterization and stem rust resistance of five wheat-Thinopyrum ponticum partial amphiploids. Journal of Genetics and Genomics. 41:591-599.
Babiker, E.M., Gordon, T.C., Obert, D.E., Jackson, E.W., Harrison, S.A., Chao, S., Carson, M.L., Bonman, J.M. 2015. Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata. Phytopathology. 105(2):239-245.
Echeverry-Solarte, M., Kumar, A., Kianian, S., Simsek, S., Alamri, M.S., Mantovani, E.E., Mcclean, P.E., Deckard, E.L., Elias, E., Schatz, B., Xu, S.S., Mergoum, M. 2015. New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary x non-supernumerary spikelet genotypes. Theoretical and Applied Genetics. 128:893-912.
Gao, Y., Faris, J.D., Liu, Z., Kim, Y.M., Syme, R.A., Oliver, R.P., Xu, S.S., Friesen, T.L. 2015. Identification and characterization of the SnTox6-Snn6 interaction in the Parastagonospora nodorum-wheat pathosystem. Molecular Plant-Microbe Interactions. 28(5):615-625.
Lu, S., Turgeon, B.G., Edwards, M.C. 2015. A ToxA-like protein from Cochliobolus heterostrophus induces light-dependent leaf necrosis and acts as a virulence factor with host selectivity on maize. Fungal Genetics and Biology. 81:12-24.
Li, G., Wang, Y., Chen, M., Edae, E.A., Poland, J.A., Akhunov, E., Chao, S., Bai, G., Carver, B.F., Yan, L. 2015. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. Biomed Central (BMC) Genomics. 16:108. doi:10.1186/s12864-015-1297-7.