Progress 04/15/13 to 02/28/18
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Accomplishments 01 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. 02 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. 03 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. 04 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. 05 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.
Impacts
(N/A)
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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. 10.1007/s00122-018-3116- 4.
- 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.
- 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).
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Accomplishments 01 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. 02 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. 03 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. 04 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. 05 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. 06 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.
Impacts
(N/A)
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.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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 01 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. 02 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. 03 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. 04 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. 05 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. 06 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.
Impacts
(N/A)
Publications
- 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.
- 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.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. 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. Accomplishments 01 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. 02 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. 03 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. 04 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. 05 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. 06 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.
Impacts
(N/A)
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.
- 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 �-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.
- 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.
- 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.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): 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 (from AD-416): 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. The wheat Snn1 gene, which confers sensitivity to a toxin produced by the fungal pathogen Stagonospora nodorum, was cloned using a molecular genetics approach. Candidate genes were identified and validated by mutagenesis. The gene is a member of the wall-associated kinase class of receptors. Snn1 is tightly regulated by the circadian clock and light, and it likely arose in the tetraploid progenitor of common wheat. This work relates directly to objective 3. Identification of molecular markers for a new Ug99 stem rust resistance gene in goatgrass. A total of 710 progeny plants from a cross between resistant and susceptible goatgrass (Ae. tauschii) accessions were evaluated for reaction to stem rust at the seedling stage, and then a subset of 179 susceptible plants were selected to conduct molecular genetic analysis to identify the chromosomal location of the gene conferring stem rust resistance. A single dominant gene for resistance was mapped to the short arm of wheat chromosome 2D. Five molecular markers were then developed for the gene region based on sequencing resources. This work relates directly to objective 2. Development of hard red spring wheat lines nearly isogenic for S. nodorum toxin sensitivity genes. The synthetic hexaploid wheat line LDNsyn2377, wheat line AF89, and tetraploid wheat line LP749-29, which carry the toxin sensitivity genes Snn3-D1, Snn4, and Snn5, respectively, were used as donors of the three genes in backcrosses to BR34 as the recurrent parent. The first generation progeny from each of backcrosses were directly evaluated for reactions to respective toxins and second generation progeny for the three genes were produced. This work relates directly to objective 4. A set of 497 landrace and cultivated durum wheat accessions deposited at the USDA-ARS National Small Grains Collection, Aberdeen, ID, was evaluated for resistance to stem rust and leaf rust pathogens. Stem rust resistance was evaluated both at the seeding stage against three races at the Cereal Disease Lab, St. Paul, MN, and at the adult plant stage under field conditions in Ethiopia. Leaf rust resistance was also evaluated both at the seedling stage against a virulent race at CIMMYT in Mexico, and at the adult plant stage in the field at ICARDA, Morocco. Results from preliminary association mapping analysis have revealed novel resistance loci against these two diseases. Lines resistant to both diseases have also been identified. This work relates directly to Objective 1. A method based on determining the DNA sequence of many small, targeted regions of the barley genome was developed and optimized to replace Illumina's GoldenGate assay containing 384 molecular markers known as single nucleotide polymorphism (SNP) markers. The targeted regions were selected based on the known DNA sequences obtained from previous screening of barley lines. Bioinformatics pipelines were developed to evaluate and analyze the sequence data from the targeted regions for marker development. The information and technology was then used to genotype barley breeding populations to support breeders' genomic selection efforts. This work relates to Objective 4. Accomplishments 01 Characterization of a wheat protein mediating sensitivity to a fungal toxin. ToxA is a fungal protein that is toxic to wheat plants and a major determinant of some fungal diseases, but how this protein becomes toxic to wheat is still not well understood. ARS researchers in Fargo, ND, identified a protein in wheat that physically interacts with the ToxA protein, and when this interaction occurs it results in plant cell death followed by disease, which leads to yield losses. These findings provide the first evidence that certain fungal proteins may act as toxins by targeting specific plant proteins to induce cell death, which might be essential for the toxin-producing fungi to colonize the host plants. These studies will help to develop better strategies to combat fungal pathogens that exploit plant proteins to cause diseases. 02 Evaluation and characterization of wheatgrass for resistance to stem rust disease of wheat. Among the relative species of wheat, several wild species belonging to the genus Thinopyrum (common name: wheatgrass) have been used as sources of resistance to rusts and other major diseases in wheat. In an effort to identify novel sources of resistance to stem rust race Ug99, ARS researchers at Fargo, ND and St. Paul, MN, evaluated 241 lines representing five different wheatgrass species for reaction to nine different strains of the stem rust pathogen. The results showed that all but one line were resistant to most of the stem rust strains. The lines with high levels of resistance to Ug99 are useful sources of stem rust resistance for wheat improvement. 03 Evaluation of durum wheat proteins on bread making quality. Durum wheat has traditionally been used to make pasta, but it would be advantageous if it could be marketed for bread making as well. ARS researchers at Fargo, ND investigated the effects of protein composition on bread making quality in durum. The proteins studied included glutenin (one of the two protein components of gluten), identified as bands 5+10 and band 8, and two groups of small glutenin proteins identified as LMWI or LMWII. Durum that had bands 5+10 had higher glutenin content, which was associated with exceedingly strong dough, and absence of band 8 resulted in weaker dough. Durum having LMWI had weaker dough than those having LMWII. This study provides useful knowledge for improving durum bread making quality by selecting optimal combinations of protein components. 04 Identification of genes associated with head shape in wheat. The wheat head is important because it is where reproduction occurs and it holds the seeds until harvest. ARS researchers at Fargo, ND, investigated genes from a wild wheat relative that govern a shorter, more compact wheat head. Two different genes, one associated with head length and another associated with the number of seed-bearing bodies per head, were both located to a single chromosome. These genes and the traits they are associated with may be useful for improving drought resistance in modern durum varieties. 05 Identification of a gene mutation critical for the domestication of wheat. The domestication of wheat was instrumental in spawning the civilization of humankind, and it occurred through genetic mutations that gave rise to types with non disarticulating heads, soft glumes, and free-threshing seed, which are traits that made wheat easy to cultivate, harvest, and thresh for early farmers. ARS researchers at Fargo, ND, identified and analyzed a gene from the ancestor of the maternal parent of common wheat known as wild emmer that prohibits the seed from being easily threshed. The research showed that this gene underwent mutation about 8,000 years ago to give rise to our modern free-threshing wheats. Knowledge of the evolutionary events leading to modern day varieties will be useful for devising novel strategies for wheat improvement. 06 Characterization of zinc-DNA interactions potentially involved in wheat genome evolution. The genomes of organisms contain DNA sequences that make up genes, but also repetitive, or so-called "junk," DNA, and the origins and roles of the latter are poorly understood. The wheat genome contains particularly large amounts of "junk" DNA. An ARS researcher in Fargo, ND, conducted DNA analysis of genes in wheat and found that the annealing of complementary DNA sequences (a crucial step in DNA synthesis, repair and recombination) was blocked by zinc, an essential trace element. However, "junk" DNA was resistant to zinc blocking. These findings suggest that zinc-DNA interactions might be among natural forces driving "junk" DNA prevalence in the genome. Further studies may provide further understanding of the evolution of economically important traits such as disease resistance governed by genes associated with "junk" DNA in wheat.
Impacts
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Publications
- Niu, Z., Klindworth, D.L., Yu, G., Friesen, T.L., Chao, S., Jin, Y., Cai, X., Ohm, J.-B., Rasmussen, J.B., Xu, S.S. 2014. Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum. Theoretical and Applied Genetics. 127:969-980.
- Faris, J.D., Zhang, Z., Garvin, D.F., Xu, S.S. 2014. Molecular and comparative mapping of genes governing spike compactness inherited from wild emmer wheat. Molecular Genetics and Genomics. 289:641-651.
- Faris, J.D., Zhang, Z., Chao, S. 2014. Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication. Gene. 542:198-208.
- Klindworth, D.L., Hareland, G.A., Elias, E.M., Ohm, J.-B., Puhr, D.P., Xu, S.S. 2014. Interactions of genotype and glutenin subunit composition on breadmaking quality of durum 1AS�1AL-1DL translocation lines. Cereal Chemistry. 91(3):211-217.
- Niu, Z., Jiang, A., Abu Hammad, W., Oladzadabbasabadi, A., Xu, S.S., Mergoum, M., Elias, E.M. 2014. Review of doubled haploid production in durum and common wheat through wheat x maize hybridization. Plant Breeding. 133:313-320.
- Niu, Z., Puri, K.D., Chao, S., Jin, Y., Sun, Y., Steffenson, B.J., Maan, S. S., Xu, S.S., Zhong, S. 2013. Genetic analysis and molecular mapping of crown rust resistance in common wheat. Theoretical and Applied Genetics. 127:609-619.
- Bassi, F.M., Kumar, A., Zhang, Q., Paux, E., Huttner, E., Kilian, A., Dizon, R., Feuillet, C., Xu, S.S., Kianian, S.F. 2013. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. Theoretical and Applied Genetics. 126:1977-1990.
- Faris, J.D., Liu, Z.H., Xu, S.S. 2013. Genetics of tan spot resistance in wheat. Theoretical and Applied Genetics. 126:2197-2217.
- Mujeeb-Kazi, A., Kazi, A.G., Dundas, I., Rasheed, A., Bux, H., Chen, P., Wang, R., Xu, S.S., Mahmood, T. 2013. Genetic diversity for wheat improvement as a conduit to food security. Advances in Agronomy. 122:179- 258.
- Ogbonnaya, F.C., Abdalla, O., Kazi-Mujeeb, A., Kazi, A.G., Xu, S.S., Gosman, N., Lagudah, E.S., Bonnett, D., Sorrells, M.E. 2013. Synthetic hexaploids: Harnessing species of the primary gene pool for wheat improvement. Plant Breeding Reviews. 37:35-122.
- Suttle, J.C., Huckle, L.L., Lu, S., Knauber, D.C. 2014. Potato tuber cytokinin oxidase/dehydrogenase genes: Biochemical properties, activity, and expression during tuber dormancy progression. Journal of Plant Physiology. 171:448-457.
- Li, C., Chen, M., Chao, S., Yu, J., Bai, G. 2012. Identification of a novel gene, H34, in wheat using recombinant inbred lines and single nucleotide polymorphism markers. Theoretical and Applied Genetics. 126:2065-2017.
- Somo, M., Chao, S., Acevedo, M., Zurn, J., Cai, X., Marais, F. 2014. A genomic comparison of homoeologous recombinants of the Lr19 (T4) translocation in wheat. Crop Science. 54:565-575.
- Lu, S. 2014. Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner. Scientific Reports. 4:5464. Available:
- Liu, S., Yang, X., Zhang, D., Bai, G., Chao, S., Bockus, W. 2014. Genome- wide association analysis identified SNPs closely linked to a gene resistant to Soil-borne wheat mosaic virus. Theoretical and Applied Genetics. 127:1039-1047.
- Lu, Y., Wang, M., Chen, X., See, D.R., Chao, S., Jing, J. 2014. Mapping of Yr62 and a small effect QTL for high-temperature adult-plant resistance to stripe rust in spring wheat PI 192252. Theoretical and Applied Genetics. 127:1449-1459.
- Munoz-Amatrian, M., Cuesta-Marcos, A., Endelman, J.B., Comadran, J., Bonman, J.M., Bockelman, H.E., Chao, S., Russell, J., Waugh, R., Hayes, P. M., Muehlbauer, G.J. 2014. The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One. 9(4):394688. doi:10.137/journal. pone.0094688.
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