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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

2017 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
Characterization of domestication genes in cultivated emmer wheat. Cultivated emmer is a relative of wheat that provides a vast source of genetic variation useful for the improvement of modern wheat varieties. Knowledge of the genes that underwent mutation in cultivated emmer to give rise to modern domesticated wheat would be useful to help exploit the reservoir of genetic variation. The genes associated with domestication are being evaluated in both cultivated emmer and modern durum wheat to determine their effects and impact on domestication. Knowledge generated from this work will allow researchers to utilize the genetic information from cultivated emmer wheat more efficiently for durum and common wheat improvement. This work directly relates to objective 1. Identification of a major tan spot resistance gene in wild emmer wheat. Tan spot is a significant foliar disease of durum and common wheat. A gene with major effects for resistance to all known strains of the tan spot pathogen was identified in an accession of wild emmer wheat. Genetic markers were developed for the gene, and the gene is currently being introgressed into modern durum varieties. The identification and deployment of this gene will provide high levels of tan spot resistance in both common and durum wheat. This work directly relates to objective 2. Development of wheat lines for evaluating the effects of seed dormancy genes from wild emmer wheat. Durum wheat cultivars carrying genes affecting seed dormancy can help reduce pre-harvest sprouting damage during wet harvesting conditions. Two genes of wild emmer origin with large effects on seed dormancy were previously identified and their chromosomal locations determined. Conventional breeding practices were used to move the two genes into two North Dakota durum wheat cultivars, Ben and Grenora, which are highly susceptible to pre-harvest sprouting. DNA markers were applied to assist with line selection throughout the breeding process. The resulting lines were evaluated in the field in 2017. These lines will be useful for determining the precise genetic effects of the dormancy genes, and how the genes will affect modern durum wheat varieties. This work directly relates to objective 2. Characterization of fungal genes associated with Fusarium head blight (FHB). FHB is a devastating disease of wheat worldwide that is caused mainly by the fungal pathogen Fusarium graminearum. Sets of genes harbored by the fungus were evaluated for their role in aiding the fungus to cause disease. One gene was found to substantially contribute to causing disease on particular wheat varieties. Further study of this fungal gene would help to reveal how the fungus causes FHB in wheat, and help researchers develop wheat varieties with enhanced FHB resistance. This work relates to objective 3. Development of elite durum wheat lines with Fusarium head blight (FHB) resistance. Over 200 elite durum lines with different levels of FHB resistance have been developed. Four of these durum lines exhibited a high level of FHB resistance and excellent agronomic traits. These lines will be useful for developing FHB-resistant cultivars in durum wheat breeding programs. This work relates directly to objective 4. Development of durum and bread wheat lines 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. Backcrossing of Sr47 into durum (Tioga, Carpio, and Joppa) and bread wheat cultivars and lines has been completed. The lines are currently being tested for yield in field trials. These lines will be useful for developing Ug99-resistant cultivars in durum and bread wheat breeding programs. This work relates directly to objective 4.

1. Identification of a novel disease susceptibility gene in wheat. Septoria nodorum blotch (SNB) is a severe fungal disease of wheat worldwide. ARS researchers at Fargo, North Dakota isolated a new gene in wheat known as Snn1, which makes wheat susceptible to SNB. The researchers found that Snn1 is somewhat of a sentinel to detect invading biotrophic pathogens, and subsequently alerts other genes to activate a defense. As part of this defense, the plant kills an area of its own tissue where the pathogen has penetrated in an attempt to localize the pathogen and prohibit its growth. However, what the plant does not realize is that the pathogen, being a necrotroph, has the ability to live, and even thrive, on the dead tissue, and so the more the plant tries to defend itself, the more the pathogen can grow and cause disease. This knowledge will allow researchers to devise novel strategies to combat crop losses to the types of pathogens known as necrotrophs.

2. The characterization of a disease susceptibility gene in durum wheat. Tan spot and Septoria nodorum blotch (SNB) are serious fungal diseases of wheat worldwide that cause substantial yield losses. Previous research has shown that both fungal pathogens produce a protein known as ToxA that, when recognized by the durum wheat gene Tsn1, causes the wheat cells to die. ARS researchers at Fargo, North Dakota conducted in-depth studies of the Tsn1-ToxA interaction between durum wheat infected with either the tan spot or the SNB pathogen. The researchers determined that, in the presence of Tsn1, ToxA played a major role in making durum wheat more susceptible to SNB; however, it had little to no effect in making durum susceptible to tan spot. This work suggests that, despite production of the ToxA protein, the tan spot pathogen employs alternate mechanisms to cause disease in durum wheat. The knowledge gained from this work sheds light on how pathogens infect plants such as durum wheat, and it provides researchers with information to devise new strategies to combat disease.

3. Genetic characterization of genes that govern susceptibility to tan spot in wheat. Tan spot is a devastating fungal disease of wheat in many wheat-growing regions around the world. Previous research has revealed the identification of several genes, such as Tsn1 and Tsc1, which govern susceptibility to tan spot in wheat. ARS researchers in Fargo, North Dakota conducted genetic studies to determine the relationships of the susceptibility genes and their relative importance in governing tan spot susceptibility. The researchers found that both genes, when present, contribute substantially to the development of disease, and their effects are cumulative, meaning that significantly more disease occurs when both genes are present compared to when only one or the other gene is present. The results of this work demonstrates the importance of removing both Tsn1 and Tsc1 from modern wheat varieties to achieve resistance to the disease tan spot.

4. Identification of wheat lines resistant to the disease Fusarium head blight (FHB). The fungal disease FHB continues to pose a major threat to the wheat production regions in the U.S. To develop wheat cultivars with better resistance, it is necessary to evaluate and identify germplasm carrying novel resistance genes. ARS researchers in Fargo, North Dakota developed a set of wheat lines by crossing various durum wheat accessions with goatgrass, a wild relative of wheat, and evaluated the lines for resistance to FHB in both greenhouse and field nurseries. At least thirteen lines showed high levels of FHB resistance and should prove to be useful resources for wheat improvement.

5. Identification of a novel class of pathogen defense-related genes in wheat. A group of plant genes known as pathogenesis-related (PR-1) genes are known to produce proteins that operate outside of individual plant cells, and they help the plant resist invading pathogens by perceiving pathogen-secreted molecules. However, it is unknown how the recognition of the pathogen molecules by the PR-1 proteins is relayed to other plant genes to mount a resistance response. ARS researchers at Fargo, North Dakota, identified two novel genes from wheat that each contain PR-1 gene-like features, and they also each contain a second feature known as a kinase, which is known to be a critical component in signal transduction pathways related to plant defense. This work provides the first evidence for a direct link between PR-1 function and signal transduction pathways in plants. Further studies will help to identify additional components of the signal transduction pathways leading to disease resistance in crop plants.

6. Characterization of synthetic hexaploid wheat (SHW) for resistance to stem rust. Stem rust is historically the most damaging fungal disease of wheat globally. The newly-emerged stem rust races, such as Ug99 in Africa, are currently a serious threat to world wheat production. In a search for new sources of stem rust resistance, ARS researchers in Fargo, North Dakota and St Paul, Minnesota evaluated stem rust reactions of about 200 SHW lines, which were created by crossing durum wheat lines to several lines of a wheat progenitor species (Aegilops tauschii). Although a lack of, or reduction of, stem rust resistance derived from durum wheat in the SHW lines was common, the researchers found that a few of the SHW lines maintained the levels of resistance derived from their parents. The resistant SHW lines identified in this research will prove valuable for improving bread wheat resistance to Ug99, and the knowledge gained from this work sheds light on how genes derived from different sources influences the expression of stem rust resistance.

Review Publications
Aoun, M., Breiland, M., Turner, M.K., Loladze, A., Chao, S., Xu, S.S., Ammar, K., Anderson, J.A., Kolmer, J.A., Acevedo, M. 2016. Genome-wide association mapping of leaf rust response in a durum wheat worldwide germplasm collection. The Plant Genome. 9(3). doi:10.3835/plantgenome2016.01.0008.
Shi, G., Zhang, Z., Friesen, T.L., Raats, D., Fahima, T., Brueggeman, R.S., Lu, S., Trick, H.N., Liu, Z., Chao, W., Frenkel, Z., Xu, S.S., Rasmussen, J.B., Faris, J.D. 2016. The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease. Science Advances. 2:e1600822.
Qureshi, N., Bariana, H., Forrest, K., Hayden, M., Keller, B., Wicker, T., Faris, J.D., Salina, E., Bansal, U. 2017. Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat. Theoretical and Applied Genetics. 130:495-504.
Lu, S., Faris, J.D., Edwards, M.C. 2017. Molecular cloning and characterization of two novel genes from hexaploid wheat that encode double PR-1 domains coupled with a receptor-like protein kinase. Molecular Genetics and Genomics. 292:435-452. doi:10.1007/s00438-017-1287-3.
Virdi, S.K., Liu, Z., Overlander, M., Zhang, Z., Xu, S.S., Friesen, T.L., Faris, J.D. 2016. New insights into the roles of host gene-necrotrophic effector interactions in governing susceptibility of durum wheat to tan spot and Septoria nodorum blotch. Genes, Genomes, Genetics. 6:4139-4150. doi: 10.1534/g3.116.036525.
Feng, J., Wang, M., Chen, X., See, D.R., Zheng, Y., Chao, S., Wan, A. 2015. Molecular mapping of YrSP and its relationship with other genes for stripe rust resistance in wheat chromosome 2BL. Phytopathology. 105(9):1206-1213.
Li, C., Bai, G., Carver, B., Chao, S., Wang, Z. 2015. Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat. The Crop Journal. (2016) 4: 1-11.
Bai, G., Li, C., Carver, B., Chao, S., Wang, Z. 2016. Mapping quantitative trait loci for plant adaptation and morphology traits in wheat using single nucleotide polymorphisms. Euphytica. 208:299-312. doi:10.1007/s10681-015-1594-x.
Bulli, P., Zhang, J., Chao, S., Chen, X., Pumphrey, M. 2016. Genetic architecture of resistance to stripe rust in a global winter wheat germplasm collection. G3, Genes/Genomes/Genetics. doi: 10.1534/g3.116.028407.
Chaffin, A.S., Huang, Y., Smith, S., Bekele, W.A., Babiker, E.M., Gnanesh, B.N., Foresman, B.J., Blanchard, S.G., Jay, J.J., Reid, R.W., Wight, C.P., Chao, S., Oliver, R., Islamovic, E., Kolb, F.L., McCartney, C., Mitchell Fetch, J.W., Beattie, A.D., Bjornstad, A., Bonman, J.M., Langdon, T., Howarth, C.J., Brouwer, C.R., Jellen, E.N., Esvelt Klos, K.L., Poland, J., Hsieh, T., Brown, R., Jackson, E., Schlueter, J.A., Tinker, N.A. 2016. A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial sub-genome rearrangement. The Plant Genome. 9(2). doi: 10.3835/plantgenome2015.10.0102.
Gao, Y., Liu, Z., Faris, J.D., Richards, J., Brueggeman, R.S., Li, X., Oliver, R.P., McDonald, B.A., Friesen, T.L. 2016. Validation of genome-wide association studies as a tool to identify virulence factors in Parastagonospora nodorum. Phytopathology. 106(10):1177-1185.
Li, C., Bai, G., Chao, S., Wang, Z. 2016. A high-density SNP and SSR consensus map reveals segregation distortion regions in wheat. BioMed Research International. doi:10.1155/2015/830618.
Tiwari, V.K., Faris, J.D., Friebe, B., Gill, B.S. 2016. Genome mapping. In: Wrigley, C., Walker, C.E., Corke, H., editors. Encyclopedia of Grain Science. Waltham, MA: Academic Press. pp. 365-375.
Winkler, L., Bonman, J.M., Chao, S., Yimer, B.A., Bockelman, H.E., Esvelt Klos, K.L. 2016. Population structure and genotype-phenotype associations in a collection of oat landraces and historic cultivars. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01077.
Xu, S.S., Liu, Z., Zhang, Q., Niu, Z., Jan, C., Cai, X. 2016. Chromosome Painting by GISH and Multicolor FISH. In: Kianian, S.F., Kianian, P.M.A., Editors. Plant Cytogenetics: Methods and Protocols. Methods in Molecular Biology. New York: Springer. p. 7-21.
Nirmala, J.H., Chao, S., Olivera, P., Babiker, E.M., Abeyo, B., Tadesse, Z., Imtiaz, M., Talbert, L., Blake, N., Akhunov, E., Pumphrey, M.O., Jin, Y., Rouse, M.N. 2016. Markers linked to wheat stem rust resistance gene Sr11 effective to Puccinia graminis f. sp. tritici race TKTTF. Phytopathology. 106(11):1352-1358.
Klindworth, D.L., Saini, J., Long, Y., Rouse, M.N., Faris, J.D., Jin, Y., Xu, S.S. 2017. Physical mapping of DNA markers linked to stem rust resistance gene Sr47 in durum wheat. Theoretical and Applied Genetics. 130:1135-1154. doi: 10.1007/s00122-017-2875-7.
Harris, M.O., Jacob, J., Brown, P., Anderson, K., El-Bouhssini, M., Peairs, F., Yan, G., Hein, G., Xu, S.S. 2017. Wheat pests: Rodents, nematodes, insects and mites. In: Langridge, P., editor. Achieving Sustainable Cultivation of Wheat. Volume 1: Breeding, Quality Traits, Pests and Diseases. Cambridge, UK: Burleigh Dodds Science Publishing Limited. p. 467-544.
Liu, Z., Zurn, J.D., Kariyawasam, G., Faris, J.D., Shi, G., Hansen, J., Rasmussen, J.B., Acevedo, M. 2017. Inverse gene-for-gene interactions contribute additively to tan spot susceptibility in wheat. Theoretical and Applied Genetics. 130:1267-1276. doi: 10.1007/s00122-017-2886-4.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Brown Guedira, G.L., Pretorius, Z.A., Wanyera, R., Newcomb, M., Bonman, J.M. 2016. Genetic mapping of resistance to the Ug99 race group of Puccinia graminis f. sp tritici in a spring wheat landrace CItr 4311. Theoretical and Applied Genetics. 129(11):2161-2170.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Jin, Y., Bhavani, S., Wanyera, R., Newcomb, M., Bonman, J.M. 2017. Genetic loci conditioning adult plant resistance to the Ug99 race group and seedling resistance to races TRTTF and TTTTF of the stem rust pathogen in wheat landrace CItr 15026. Plant Disease. 101(3):496-501.
Babiker, E.M., Gordon, T.C., Chao, S., Rouse, M.N., Acevedo, M., Wanyera, R., Brown Guedira, G.L., Bonman, J.M. 2017. Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and identification of SNP marker linked to stem rust resistance gene Sr28. Phytopathology. 107(2):208-215.
Long, Y.M., Chao, W.S., Ma, G.J., Xu, S.S., Qi, L.L. 2017. An innovative SNP genotyping method adapting to multiple platforms and throughputs. Theoretical and Applied Genetics. 130(3):597-607.
Zhang, W., Cao, Y., Zhang, M., Zhu, X., Ren, S., Long, Y., Gyawali, Y., Chao, S., Xu, S., Cai, X. 2017. Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat. Crop Science. 57:1189-1198. doi: 10.2135/cropsci2016.09.0819.