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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

2016 Annual Report


Objectives
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.


Approach
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 the function of the Tsn1 gene in tetraploid wheat in response to tan spot and Septoria nodorum blotch. The effects of the Tsn1 gene in conferring susceptibility to the ToxA-producing fungal pathogens that cause tan spot and Septoria nodorum blotch in tetraploid wheat were evaluated. The data is being analyzed to determine if the Tsn1-ToxA interaction plays a different role in conferring susceptibility to tan spot as compared to Septoria nodorum blotch in tetraploid wheat. This work directly relates to objective 3. Development of markers for the tan spot susceptibility gene Tsc1 in wheat. The Tsc1 gene is known to confer susceptibility to strains of the tan spot fungus that produce the protein Ptr ToxC. Saturation mapping of the Tsc1 locus was conducted to identify and develop molecular markers closely linked to the Tsc1 gene. More than a dozen markers tightly linked to Tsc1 were developed and will be useful for map-based cloning of Tsc1 and for breeder to use as tools to select against the gene to develop tan spot resistant wheat varieties. This work directly relates to objective 2. Identification of wheat genes potentially mediating disease susceptibility in wheat. PR-1 genes are known to be involved in plant defense pathways and certain PR-1 proteins have been shown to mediate fungal disease by directly interacting with pathogen-derived effector proteins. Two new members of the wheat PR-1 gene family were cloned and found to encode novel PR-1 proteins coupled with transmembrane protein kinase known to be components of signal transduction pathways. These novel PR-1 proteins are being tested to determine if they interact with fungal effector proteins such as ToxA. This work directly relates to objective 3. Development of a marker set for marker-based breeding projects using a single nucleotide polymorphism (SNP) assay in wheat. A SNP genotyping assay was optimized for markers linked to agronomic traits such as quality, disease resistance, plant height and photoperiod. It has been used to genotype spring wheat breeding populations and regional nursery entries. The SNP assay developed for a marker linked to low grain cadmium in durum wheat has been used in breeding for improved grain cadmium content, and assisted in a new durum wheat cultivar release with low cadmium. This work relates directly to objective 4. Development of adapted solid-stem durum germplasm for resistance to sawfly. The durum landrace 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. The last two backcrosses (BC5 and BC6) were made using the six durum cultivars (Albabo, Divide, Grenora, Tioga, Carpio, and Joppa) as the recurrent parents to introgress the solid stem trait into the six durum cultivars. 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. Backcrossing of Sr47 into durum cultivars Tioga, Carpio, and Joppa has been completed and plants homozygous for Sr47 have been selected. Backcrossing of Sr47 into eight elite bread wheat cultivars and lines has been completed for 21 of the 24 populations. This work relates directly to objective 4.


Accomplishments
1. Identification of novel genes for resistance to stem rust in durum wheat. Many North American durum wheat lines are resistant to the strain of stem rust known as Ug99 because they possess a resistance gene known as Sr13. However, two new variants of Ug99 recently emerged in East Africa and are able to cause disease on durum wheat lines that have Sr13. ARS researchers at Fargo, North Dakota, in collaboration with an ARS scientist at St. Paul, Minnesota, screened a collection of 429 durum lines and identified five that were resistant to the new variants as well as the original Ug99 strains. Genetic analysis further revealed that the five lines contained several novel stem rust resistance genes. These results provided wheat breeders with valuable resources for improving stem rust resistance.

2. 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 identified a new gene in wheat that makes it susceptible to SNB. They also developed molecular markers that can be used by wheat breeders to monitor the presence of the gene among their breeding lines, which will help them to rid the gene from varieties to be released to farmers and growers.

3. The characterization of a disease susceptibility gene in wheat. Septoria nodorum blotch (SNB) is a serious fungal disease of wheat worldwide that causes substantial yield losses. Previous research has shown that the fungus exploits specific ‘susceptibility’ genes in wheat to cause disease. ARS researchers at Fargo, North Dakota conducted in-depth studies of one such susceptibility gene known as Snn3. The researchers determined the precise location of the gene within the wheat genome and developed molecular markers that can be used to monitor the gene and its presence among wheat lines. This work provides breeders with the ability to use the markers to efficiently remove the gene from their breeding lines, and it sets the stage for revealing the identity of Snn3, which will shed light on how the fungus exploits it to cause disease.

4. Identification of a novel gene for resistance 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 uncovered several genes in wheat that govern low-levels of tan spot resistance, or resistance to only specific strains of the fungus. ARS researchers in Fargo, North Dakota identified a new tan spot resistance gene in a wild relative of wheat that conditions high-levels of resistance to all known strains of the tan spot fungus. The deployment of this gene into commercial wheat varieties should greatly reduce the economic losses attributed to this disease.

5. Development of molecular markers for the stem rust resistance gene Sr47. The wheat gene Sr47, which was previously transferred from goatgrass into durum wheat, is highly effective in conferring resistance to all strains of the fungal pathogen that cause the disease stem rust. However, molecular markers, which can be used by plant breeders to efficiently monitor the transfer of the gene through crossing into elite lines, have not yet been developed for Sr47. ARS researchers at Fargo, North Dakota and their collaborators at North Dakota State University develop four new molecular markers that are tightly associated with Sr47. These new markers will greatly facilitate the transfer and deployment of Sr47 in durum and bread wheat breeding, which will lead to the development of stem rust resistant varieties.

6. Identification of pathogen-derived proteins associated with Fusarium head blight disease in wheat. Head blight is a devastating disease of wheat worldwide. The mechanisms associated with plant resistance to this disease are not well understood. ARS researchers in Fargo, North Dakota identified dozens of genes from the causal fungus Fusarium graminearum that encode proteins potentially involved in host-pathogen interactions. Further study of these fungal proteins will help to identify plant molecules involved in resisting head blight disease in wheat.


Review Publications
Zhu, X., Zhong, S., Chao, S., Gu, Y.Q., Kianian, S.F., Elias, E., Cai, X. 2016. Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat. Theoretical and Applied Genetics. 129:31-43.
Chao, S., Elias, E., Benscher, D., Ishikawa, G., Huang, Y.-F., Saito, M., Nakamura, T., Xu, S., Faris, J., Sorrells, M. 2016. Genetic mapping of major-effect seed dormancy quantitative trait loci on chromosome 2B using recombinant substitution lines in tetraploid wheat. Crop Science. 56:59-72.
Lu, S., Edwards, M.C. 2016. Genome-wide analysis of small secreted cysteine-rich proteins identifies candidate effector proteins potentially involved in Fusarium graminearum-wheat interactions. Phytopathology. 106:166-176.
Gao, L., Kielsmeirer-Cook, J., Bajgain, P., Zhang, X., Chao, S., Rouse, M.N., Anderson, J.A. 2015. Development of genotyping by sequencing (GBS)- and array-derived SNP markers for stem rust resistance gene Sr42. Molecular Breeding. 35:207.
Gao, L., Turner, M.K., Chao, S., Kolmer, J., Anderson, J.A. 2016. Genome wide association study of seedling and adult plant leaf rust resistance in elite spring wheat breeding lines. PLoS ONE. 11(2):e0148671.
Zurn, J.D., Newcomb, M.S., Rouse, M.N., Jin, Y., Shiaoman, C., Sthapit, J., See, D.R., Wanyera, R., Njau, P., Bonman, J.M., Brueggeman, R., Acevedo, M. 2014. High density mapping of a resistance gene to Ug99 from an Iranian landrace. Molecular Breeding. 34:871-881.
Babiker, E.M., Bonman, J.M., Gordon, T.C., Chao, S., Newcomb, M.S., Rouse, M.N., Jin, Y., Wanyera, R., Acevedo, M., Brown Guedira, G.L., Williamson, S. 2015. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace. Journal of Theoretical and Applied Genetics. 128:605-612. doi:10.1007/s00122-015-2456-6.
Graebner, R.C., Wise, M.L., Cuesta-Marcos, A., Geniza, M., Blake, T., Blake, V.C., Butler, J., Chao, S., Hole, D.J., Horsley, R., Jaiswal, P., Obert, D., Smith, K.P., Ullrich, S., Hayes, P.M. 2015. Quantitative trait loci associated with the tocochromanol (vitamin E) pathway in barley. PLoS One. 10(7): e0133767. DOI:10.1371/journal.pone.0133767.
Hou, L., Chen, X., Wang, M., See, D.R., Chao, S., Bulli, P., Jing, J. 2015. Mapping a large number of QTL for durable resistance to stripe rust in winter wheat Druchamp using SSR and SNP markers. PLoS One. 10(5):e0126794.
Kalous, J.R., Martin, J.M., Sherman, J.D., Heo, H.-Y., Blake, N.K., Lanning, S.P., Eckhoff, J.L.A., Chao, S., Akhunov, E., Talbert, L.E. 2015. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross. Theoretical and Applied Genetics. 128:1799-1811.
Li, C., Bai, G., Carver, B., Chao, S., Wang, Z. 2015. Single nucleotide polymorphism markers linked to QTL for wheat yield traits. Euphytica. Published online 30 May 2015. DOI: 10.1007/s10681-015-1475-3.
Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J., Moscou, M., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bartos, J., Bhat, P., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P.P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P., Lemaux, P., Mammadov, J., Close, T. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 84(1):216-227. doi: 10.1111/tpj.12959.
Shi, G., Friesen, T.L., Jyoti Saini, Xu, S.S., Rasmussen, J.B., Faris, J.D. 2015. The wheat Snn7 gene confers susceptibility on recognition of the Parastagonospora nodorum necrotrophic effector SnTox7. The Plant Genome. 8. doi: 10.3835/plantgenome2015.02.0007.
Shi, G., Zhang, Z., Friesen, T.L., Bansal, U., Cloutier, S., Wicker, T., Rasmussen, J.B., Faris, J.D. 2016. Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Molecular Genetics and Genomics. 291:107-119.
Varella, A.C., Weaver, D.K., Sherman, J.D., Blake, N.K., Heo, H.Y., Kalous, J.R., Chao, S., Hofland, M.L., Martin, J.M., Kephart, K.D., Talbert, L.E. 2015. Association analysis of stem solidness and wheat stem sawfly resistance in a panel of North American spring wheat germplasm. Crop Science. 55:2046-2055.
Yu, G., Klindworth, D.L., Friesen, T.L., Faris, J.D., Zhong, S., Rasmussen, J.B., Xu, S.S. 2015. Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat. Theoretical and Applied Genetics. 128:2367-2374.
Zheng, Q., Luo, Q., Niu, Z., Li, H., Li, B., Xu, S.S., Li, Z. 2015. Variation in chromosome constitution of the Xiaoyan series partial amphiploids and its relationship to stripe rust and stem rust resistance. Journal of Genetics and Genomics. 42:657-660.
Babiker, E.M., Bonman, J.M., Gordon, T.C., Chao, S., Rouse, M.N., Brown Guedira, G.L., Williamson, S., Pretorius, Z.A. 2016. Rapid identification of resistance loci effective against Puccinia graminis f. sp. tritici race TTKSK in 33 spring wheat landraces. Plant Disease. 100(2):331-336.
Edwards, M.C., Weiland, J.J., Todd, J., Stewart, L.R., Lu, S. 2016. ORF43 of maize rayado fino virus is dispensable for systemic infection of maize and transmission by leafhoppers. Virus Genes. 52:303-307.
Garvin, D.F., Porter, H., Blankenheim, Z., Chao, S., Dill-Macky, R. 2015. A spontaneous segmental deletion from chromosome arm 3DL enhances Fusarium head blight resistance in wheat. Genome. 58(11):479-488.
Kariyawasam, G.K., Carter, A.H., Rasmussen, J.B., Faris, J., Xu, S.S., Mergoum, M., Liu, Z. 2016. Genetic relationships between race-nonspecific and race-specific interactions in the wheat-Pyrenophora tritici-repentis pathosystem. Theoretical and Applied Genetics. 129:897-908. doi: 10.1007/s00122-016-2670-x.
Liu, Z., Gao, Y., Kim, Y.M., Faris, J.D., Shelver, W.L., de Wit, P.J.G.M., Xu, S.S., Friesen, T.L. 2016. SnTox1, a Parastagonospora nodorum necrotrophic effector, is a dual-function protein that facilitates infection while protecting from wheat-produced chitinases. New Phytologist. 211:1052-1064. doi: 10.1111/nph.13959.
Su, Z., Jin, S., Yue, L., Zhang, G., Chao, S., Bai, G. 2016. Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat. Molecular Breeding. 36: 15. doi:10.1007/s11032-016-0436-4.
Islamovic, E., Obert, D.E., Oliver, R., Marshall, J.M., Miclaus, K.J., Hang, A., Chao, S., Lazo, G.R., Harrison, S.A., Ibrahim, A., Jellen, E.N., Maughan, P.J., Brown, R.H., Jackson, E.W. 2013. A new genetic linkage map of barley (Hordeum vulgare L.) facilitates genetic dissection of height and spike length and angle. Field Crops Research. 154:91-99.
Faris, J.D. 2014. Wheat domestication: Key to agricultural revolutions past and future. In: Tuberosa, R., Graner, A., Frison, E., editors. Genomics of Plant Genetic Resources. Volume 1. Managing, Sequencing and Mining Genetic Resources. Springer. p. 439-464.
Chao, S., Lawley, C. 2015. Use of the Illumina GoldenGate assay for single nucleotide polymorphism (SNP) genotyping in cereal crops. In: Batley, J., editor. Plant Genotyping: Methods and Protocols, Methods in Molecular Biology. Volume 1245. New York, NY: Springer Science+Business Media. p. 299-312. doi: 10.1007/978-1-4939-1966-6.
Zhang, P., Dundas, I.S., Mcintosh, R.A., Xu, S.S., Park, R.F., Gill, B.S., Friebe, B. 2015. Chapter 9, Wheat-Aegilops introgressions. In: Ceoloni, C., Dolezel, J., Molnar-Lang, M., editors. Alien Introgression in Wheat. Switzerland: Springer International Publishing. p. 221-243.
Esvelt Klos, K.L., Huang, Y., Babiker, E.M., Beattie, A., Bekele, W.A., Bjornstad, A., Bonman, J.M., Carson, M.L., Chao, S., Gnanesh, B.N., Harrison, S.A., Howarth, C.J., Hu, G., Ibrahim, A., Islamovic, E., Jackson, E.W., Jannink, J., Kolb, F.L., Mcmullen, M.S., Fetch, J.M., Murphy, J., Obert, D.E., Ohm, H.W., Rines, H.W., Rossnagel, B., Schuleter, J.A., Wight, C.P., Yan, W., Tinker, N.A. 2016. Population genetics related to adaptation in elite oat germplasm. The Plant Genome. 9(2):1-12. doi: 10.3835/plantgenome2015.10.0103.
Foresman, B.J., Oliver, R.E., Jackson, E.W., Chao, S., Arruda, M.P., Kolb, F.L. 2016. Genome-wide association mapping of barley yellow dwarf virus tolerance in spring oat (Avena sativa L.). PLoS ONE. 11(5):e0155376. doi: 10.1371/journal.pone.0155376.
Kippes, N., Debernardi, J.M., Vasquez-Gross, H.A., Akpinar, B.A., Budak, H., Kato, K., Chao, S., Akhunov, E., Dubcovsky, J. 2015. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. PNAS. 112(39):E5401-E5410. doi: 10.1073/pnas.1514883122.
Mergoum, M., Simsek, S., Zhong, S., Acevedo, M., Friesen, T.L., Alamri, M.S., Xu, S., Liu, Z. 2016. 'Elgin-ND' spring wheat: A newly adapted cultivar to the north-central plains of the United States with high agronomic quality performance. Journal of Plant Registrations. 10:130-134. doi: 10.3198/jpr2015.07.0044crc.
Richards, J., Chao, S., Friesen, T.L., Brueggeman, R. 2016. Fine mapping of the barley chromosome 6H net form net blotch susceptibility locus. G3. 6:1809-1818. doi: 10.1534/g3.116.028902.