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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

2018 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
This is the final report for the project 3060-21000-037-00D. Research continues under the new project 3060-21000-038-00D. Throughout the life of the project, significant progress was made in multiple areas. The following summary of progress over the life of the project relates to the achievement of the objectives of the project. Genes associated with yield, yield components, head morphology, development, and domestication of wheat were identified, mapped, and genetically characterized. Molecular markers associated with the genes governing these traits were identified, and are being used to characterize germplasm and introgress desirable alleles into new durum and common wheat cultivars. Genes governing resistance to pre-harvest sprouting were identified from wild emmer wheat and their chromosome locations were determined. Lines containing these genes are being used to enhance pre-harvest sprouting resistance levels in commercial varieties. Four new genes governing susceptibility to the wheat disease Septoria nodorum blotch were identified and mapped, and a fourth gene was cloned. The identification of new genes and the molecular cloning of the other has led to the development of molecular markers to select against susceptibility genes resulting in new germplasm with improved resistance. It has also expanded our knowledge of the host-pathogen interactions. A new gene governing broad spectrum race-nonspecific resistance to the tan spot pathogen was identified and its effects were characterized. The gene was identified in a modern wheat cultivar, which is now being used in crossing schemes to transfer to new varieties and develop tan spot resistant wheat varieties. Tan spot susceptibility genes were also characterized in durum wheat, which revealed that some compatible host-pathogen interactions in the wheat-tan spot system behave differently in durum wheat backgrounds. This revealed that the genetic mechanisms associated with tan spot susceptibility are more complex than previously thought, and that more research is needed in this area. New marker platforms, genetic maps, genotyping data, and marker-assisted selection analysis for wheat, barley, and oat were provided to the research community, and have expedited genetic research progress as well as the development of small grains varieties with improved agronomic traits. Two novel genes with their functions associated with salt stress and defense responses were identified from cultivated bread wheat as well as its wild relative progenitors. These two genes encode hybrid proteins consisting of plant defense-related PR proteins and components of signal transduction pathways that have not been reported in previous studies. The information obtained this study will help to understand the molecular basis of stress response and host-pathogen interactions known to involve plant PR proteins as described below. A plant defense-related PR protein was identified from bread wheat and confirmed to interact with ToxA, a host-specific toxin produced by the fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum, which cause tan spot and leaf blotch diseases in wheat. In addition, a ToxA-like protein was identified from a third fungal pathogen Cochliobolus heterostrophus (which causes leaf blight disease in maize) and found to act also as a host-specific virulence factor. These findings provided the research community with the first evidence that plant defense PR proteins are directly targeted by pathogen effectors and may condition disease susceptibility in cereal crops. More than 30 candidate effector proteins were identified from the fungal pathogen Fusarium graminearum, which causes Fusarium head blight (FHB) in wheat, a devastating disease of wheat and barley worldwide. Functional studies have confirmed that at least one of these candidate proteins contributes to fungal virulence in FHB development. The data obtained from these studies laid a foundation for further characterization of FHB resistance mechanisms as proposed in the renewed project. New genes controlling resistance to the African races (e.g. Ug99) of the wheat stem rust pathogen were identified from wheat relative species including wild and cultivated emmer wheat, Persian wheat, Polish wheat, and goatgrass. Molecular markers associated with these genes were identified and are being used to assist introgression of the genes into new durum and common wheat cultivars. Genes associated with resistance to Fusarium head blight were identified and mapped in cultivated emmer wheat and common wheat. Molecular markers associated with these genes were identified and are being used to assist introgression of the genes into new durum and common wheat cultivars. Elite durum wheat germplasm with FHB resistance transferred from cultivated emmer and common wheat have been developed using multiple backcrosses and selections. Four of these durum lines exhibited a high level of FHB resistance and excellent agronomic traits. These lines are being used for developing FHB-resistant cultivars in durum wheat breeding programs. Elite durum and common wheat germplasm with stem rust Ug99 resistance transferred from wild relative species of wheat have been developed using multiple backcrosses and marker-assisted selections. These lines will be useful for developing Ug99-resistant cultivars in durum and bread wheat breeding programs. The durum germplasm with solid stem for resistance to sawfly have been developed by transferring the genes for solid stem from a durum landrace into North Dakota durum cultivars. These lines are being used for developing solid-stemmed cultivars in durum wheat breeding programs.

1. Characterization of a fungal protein leading to disease in wheat. Fusarium head blight (FHB), a devastating disease of wheat crops worldwide, is caused mainly by the fungus Fusarium graminearum, which produces a number of mycotoxins harmful to humans and animals. Molecular mechanisms controlling disease capability and severity of the fungus are still not well understood. ARS researchers in Fargo, North Dakota, investigated a group of proteins in the FHB fungus that are similar to a group of proteins, known as PR proteins, that plants utilize to defend themselves against pathogens. The researchers identified one such PR protein that was partially required for the fungus to cause FHB in wheat. This work provides evidence that fungal PR proteins are involved in host-pathogen interactions like the related proteins in plants. This knowledge will help researchers devise novel strategies to control FHB disease in wheat.

2. Identification of a novel stress-responsive gene in wheat. Plants are subjected to various stress conditions such as soil salinity. Identifying genes that control salinity responses is a major goal of plant scientists. ARS researchers in Fargo, North Dakota, identified a unique gene in a wild relative of wheat (Triticum urartu) that was strongly expressed in response to elevated salt conditions. T. urartu lines lacking this gene were more sensitive to salt treatment than those carrying this gene. The work in this study will help to unravel the molecular components controlling salt tolerance and will enable the genetic improvement of crop plants in future studies.

3. Identification and mapping of stem rust resistance genes in U.S. durum germplasm. Wheat production in many wheat-growing regions is vulnerable to stem rust disease. Several previous studies showed that most of the durum wheat cultivars growing in the upper Great Plains in the U.S. have good resistance to the major stem rust races, including the devastating African race known as Ug99. However, most of the stem rust resistance genes present in the durum cultivars were previously not known. ARS researchers in Fargo, North Dakota identified four stem rust resistance genes through genetic analysis of resistance, and they developed molecular markers for three of the genes. The knowledge of the stem rust resistance genes present in U.S. durum lines and the new molecular markers will be useful for developing new durum and wheat cultivars with combinations of multiple stem rust resistance genes to better combat the disease.

4. Evaluation and characterization of Hessian fly resistance in Aegilops species. Aegilops species, commonly known as goatgrasses, are an important source of resistance genes for managing many diseases and insect pests of wheat. However, most of the collections of Aegilops species have not been evaluated and characterized for resistance to the wheat pest known as Hessian fly. ARS researchers in Fargo, North Dakota, evaluated 675 lines belonging to 11 Aegilops species and identified 155 resistant lines from eight species. Identification of these resistant lines will facilitate the discovery of novel genes for controlling this insect pest and the transfer of these resistance genes into improved wheat germplasm.

5. Transfer of a major gene for scab resistance from common wheat into durum wheat. Durum wheat production in the U.S. has been seriously jeopardized by wheat scab since the early 1990s. However, durum cultivars with high levels of scab resistance have not been available due to limited sources of scab resistance in durum breeding lines and related material. ARS researchers in Fargo, North Dakota successfully transferred a major gene for scab resistance from common wheat into durum wheat using multiple backcrosses and selections. The durum line carrying the scab resistance gene is being used by U.S. durum wheat breeding programs to develop new durum varieties and adapted germplasm with scab resistance.

Review Publications
Lu, S., Edwards, M.C. 2017. Molecular characterization and functional analysis of PR-1-like proteins identified from the wheat head blight fungus Fusarium graminearum. Phytopathology. 108:510-520.
Chen, S., Guo, Y., Briggs, J., Dubach, F., Chao, S., Zhang, W., Rouse, M.N., Dubcovsky, J. 2017. Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum. Theoretical and Applied Genetics. 131(3):625-635.
Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S.O., Gundlach, H., Hale, I., Mascher, M., Spannagl, M., Wiebe, K., Jordan, K.W., Golan, G., Deek, J., Ben-Zvi, B., Ben-Zvi, G., Himmelbach, A., MacLachlan, R.P., Sharpe, A.G., Fritz, A., Ben-David, R., Budak, H., Fahima, T., Korol, A., Faris, J.D., Hernandez, A., Mikel, M.A., Levy, A.A., Steffenson, B., Maccaferri, M., Tuberosa, R., Cattivelli, L., Faccioli, P., Ceriotti, A., Kashkush, K., Pourkheirandish, M., Komatsuda, T., Eilam, T., Sela, H., Sharon, A., Ohad, N., Chamovitz, D.A., Mayer, K.F.X., Stein, N., Ronen, G., Peleg, Z., Pozniak, C.J., Akhunov, E.D., Distelfeld, A. 2017. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science. 357:93-97.
Debernardi, J.M., Lin, H., Chuck, G., Faris, J.D., Dubcovsky, J. 2017. MicroRNA172 plays a critical role in wheat spike morphogenesis and grain threshability. Development. 144:1966-1975.
Nirmala, J.H., Chao, S., Olivera, P., Babiker, E.M., Abeyo, B., Tadesse, Z., Imtiaz, M., Talbert, L., Blake, N., Akhunov, E., Pumphrey, M., Rouse, M.N., Jin, Y. 2017. Markers linked to wheat stem rust resistance gene Sr11 effective to Puccinia graminis f. sp. tritici race TKTTF. Phytopathology. 106(11):1352-1358.
Yu, L., Chao, S., Singh, R., Sorrells, M. 2017. Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat. PLoS One. doi: 10.1371/journal.pone.0171963.
Sapkota, S., Zhang, Q., Chittem, K., Mergoum, M., Xu, S.S., Liu, Z. 2017. Evaluation of triticale accessions for resistance to wheat bacterial leaf streak caused by Xanthomonas translucens pv. undulosa. Plant Pathology. 67:595-602.
Zhang, W., Zhang, M., Zhu, X., Cao, Y., Sun, Q., Ma, G., Chao, S., Yan, C., Xu, S.S., Cai, X. 2017. Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome. Theoretical and Applied Genetics. 131:365-375.
Zhou, Y., Conway, B., Miller, D., Marshall, D.S., Cooper, A., Murphy, J.P., Chao, S., Brown Guedira, G.L., Costa, J. 2017. Quantitative trait loci mapping for spike characteristics using a genetic map with array-based and genotyping-by-sequencing (GBS) SNP markers in hexaploid wheat. The Plant Genome. https://doi:10.3835/plantgenome2016.10.0101.
Koladia, V.M., Richards, J.K., Wyatt, N.A., Faris, J.D., Brueggeman, R.S., Friesen, T.L. 2017. Genetic analysis of virulence in the Pyrenophora teres f. teres population BB25 x FGOH04Ptt021. Fungal Genetics and Biology. 107:12-19.
Nirmala, J., Saini, J., Newcomb, M., Olivera, P., Gale, S.W., Klindworth, D.L., Elias, E., Talbert, L., Chao, S., Faris, J.D., Xu, S.S., Jin, Y., Rouse, M.N. 2017. Discovery of a novel stem rust resistance allele in durum wheat that exhibits differential reactions to Ug99 isolates. G3, Genes/Genomes/Genetics.
Nirmala, J., Saini, J., Newcomb, M., Olivera, P., Gale, S.W., Klindworth, D.L., Elias, E., Talbert, L., Chao, S., Faris, J.D., Xu, S.S., Jin, Y., Rouse, M.N. 2017. Discovery of a novel stem rust resistance allele in durum wheat that exhibits differential reactions to Ug99 isolates. G3, Genes/Genomes/Genetics. 7:3481-3490.
Richards, J.K., Wyatt, N.A., Liu, Z., Faris, J.D., Friesen, T.L. 2018. Reference quality genome assemblies of three Parastagonospora nodorum isolates differing in virulence on wheat. G3, Genes/Genomes/Genetics. 8:393-399.
Saini, J., Faris, J.D., Zhang, Q., Rouse, M.N., Jin, Y., Long, Y., Klindworth, D.L., Elias, E.M., McClean, P.E., Edwards, M.C., Xu, S.S. 2018. Identification, mapping, and marker development of stem rust resistance genes in durum wheat 'Lebsock'. Molecular Breeding. 38:77.
Balcarkova, B., Frenkel, Z., Skopova, M., Abrouk, M., Kumar, A., Chao, S., Kianian, S., Akhunov, E., Korol, A., Dolezel, J., Valarik, M. 2017. A high resolution radiation hybrid map of wheat chromosome 4A. Frontiers in Plant Science. 7:2063.
Abbasabadi, A.O., Kumar, A., Pirseyedi, S., Salsman, E., Dobrydina, M., Poudel, R.S., Abuhammad, W.A., Chao, S., Faris, J.D., Elias, E.M. 2018. Identification and validation of a new source of low grain cadmium accumulation in durum wheat. G3, Genes/Genomes/Genetics. 8:923-932.
Kolmer, J.A., Chao, S., Brown Guedira, G.L., Bansal, U., Bariana, H. 2018. Adult plant leaf rust resistance derived from the soft red winter wheat cultivar Caldwell maps to chromosome 3BS. Crop Science. 58:152-158.
Lu, S., Edwards, M.C. 2018. A simple culture method inducing sexual reproduction by Fusarium graminearum, the primary causal agent of Fusarium head blight. Plant Health Progress. 19:129-130.
Lu, S., Faris, J.D., Edwards, M.C. 2018. Molecular cloning and comparative analysis of a PR-1-RK hybrid gene from Triticum urartu, the A-genome progenitor of hexaploid wheat. Plant Molecular Biology.
Aoun, M., Kolmer, J.A., Chao, S., Bulbula, W.D., Elias, E., Rouse, M.N., Acevedo, M. 2017. Inheritance and bulked segregant analysis of leaf rust and stem rust resistance genes in eight durum wheat genotypes. Phytopathology. 107:1496-1506.
Carpenter, N.R., Griffey, C.A., Malla, S., Barnett, M., Marshall, D.S., Fountain, M.O., Murphy, J.P., Milus, E., Johnson, J., Buck, J., Chao, S., Brown Guedira, G.L., Wright, E. 2017. Identification of quantitative resistance to puccinia striiformis and puccina triticina in the soft red winter wheat cultivar ‘Jamestown’. Crop Science. 57:2991-3001.
Dong, Z., Hegarty, J.M., Zhang, J., Zhang, W., Chao, S., Chen, X., Zhou, Y., Dubcovsky, J. 2017. Validation and characterization of a QTL for adult plant resistance to stripe rust on wheat chromosome arm 6BS (Yr78). Journal of Theoretical and Applied Genetics. 130(10):2127-2137.
Rines, H.W., Miller, M.E., Carson, M.L., Chao, S., Tiede, T., Wiersma, J., Kianian, S. 2017. Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa. Theoretical and Applied Genetics. 131(3):721-733.
Cook, J.P., Heo, H., Varella, A.C., Lanning, A.C., Blake, N.K., Sherman, J.D., Martin, J.M., See, D.R., Chao, S., Talbert, L.E. 2018. Evaluation of a QTL mapping population composed of hard red spring and winter wheat alleles using various marker platforms. Crop Science. 58:701-712.
Feng, J., Wang, M., See, D.R., Chao, S., Zheng, Y., Chen, X. 2018. Characterization of gene Yr79 and four additional QTL for all-stage and high-temperature adult-plant resistance to stripe rust in spring wheat PI 182103. Theoretical and Applied Genetics. 108(6):737-747.
Kolmer, J.A., Bernardo, A.N., Bai, G., Hayden, M.J., Chao, S. 2018. Adult plant leaf rust resistance derived from Toropi wheat is conditioned by Lr78 and three minor QTL. Phytopathology. 108:246-253.
Liu, L., Wang, M., Feng, J., See, D.R., Chao, S., Chen, X. 2018. Combination of all-stage and high-temperature adult-plant resistance QTL confers high level, durable resistance to stripe rust in winter wheat cultivar Madsen. Theoretical and Applied Genetics. https://doi 10.1007/s00122-018-3116-4.
Zurn, J.D., Rouse, M.N., Chao, S., Aoun, M., Macharia, G., Hiebert, C.W., Pretorius, Z.A., Bonman, J.M., Acevedo, M. 2018. Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698. BMC Genomics. 19:67.
Rutter, W.B., Salcedo, A., Akhunova, A., Wang, S., Bolus, S., Chao, S., Rouse, M.N., Szabo, L.J., Bowden, R.L., Akhunov, E., Dubcovsky, J. 2017. Variation in the AvrSr35 effector determines Sr35 resistance against wheat stem rust race Ug99. Science. 358(6370):1604-1606. https://doi:10.1126/science.aao7294.
Fiedler, J., Salsman, E., Liu, Y., Jimenez, M., Hegstad, J., Chen, B., Manthey, F.A., Chao, S., Xu, S.S., Elias, E.M., Li, X. 2017. Genome-wide association and prediction of grain and semolina quality traits in durum wheat breeding populations. The Plant Genome. 10(3).