REGIONAL BARLEY GENE MAPPING PROJECT

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: SPECIAL GRANT
• Reporting Frequency: Annual
• Accession No.: 0219290
• Grant No.: 2009-34213-19987
• Proposal No.: 2009-03386
• Project Start Date: Aug 15, 2009
• Project End Date: Aug 14, 2011
• Grant Year: 2009
• Program Code: [EI]- Regional Barley Gene Mapping Project, OR

Recipient Organization
OREGON STATE UNIVERSITY
(N/A)
CORVALLIS,OR 97331

Performing Department
Crop and Soil Science

Non Technical Summary
The Regional Barley Genome Mapping Special Grant funds the US Barley Genome Project (USBGP). The USBGP is an inter-disciplinary, multi-institutional endeavor comprised of integrated projects conducted in State Experiment Stations and Federal labs throughout the U.S. Each year, projects are selected for funding that have the potential to make a major impact on U.S. barley production, that promise to make a significant contribution to genetics, and that have the potential to leverage significant funding from other agencies. There are 10 research projects in seven states that into three general classes of endeavor for this fiscal year: "Quality means value", "Biotic Stress Resistance", and "Abiotic Stress Resistance". Barley has unique properties as a human food, as an animal feed, and - of course - as the base of beer. Researchers in Minnesota, Montana, North Dakota, and Wisconsin are leveraging Barley Coordinated Agricultural Project (CAP) funds to systematically characterize the genes, proteins, and metabolic pathways involved in malting quality in contemporary and ancestral barley germplasm. Genetic resistance is the most cost-effective and environmentally sound approach to controlling diseases. By locating and characterizing the genes that confer resistance, and understanding how these genes work, researchers in Minnesota, North Dakota, and Washington are developing tools for resistance breeding that will benefit all of American agriculture. Genetic resistance is also the most cost-effective and environmentally sound approach to dealing with abiotic stresses. Greater winterhardiness would allow barley acreage to expand into new geographic areas and assure would assure more sustainable production. By locating and characterizing the genes that confer resistance to low temperature stresses, and understanding how these genes work, researchers in Minnesota, Ohio, and Oregon are developing tools for resistance breeding that will benefit all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants.

Animal Health Component

50%

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1550	1020	25%
202	1550	1040	25%
204	1550	1080	25%
206	1550	1160	25%

Knowledge Area
206 - Basic Plant Biology; 204 - Plant Product Quality and Utility (Preharvest); 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1550 - Barley;

Field Of Science
1040 - Molecular biology; 1160 - Pathology; 1080 - Genetics; 1020 - Physiology;

Keywords

barley

genomics

nutrition

quality

resistance

Goals / Objectives
The Regional Barley Genome Mapping Special Grant funds the US Barley Genome Project (USBGP). The USBGP is an inter-disciplinary, multi-institutional endeavor comprised of integrated projects conducted in State Experiment Stations and Federal labs throughout the U.S. Each year, projects are selected for funding that have the potential to make a major impact on U.S. barley production, that promise to make a significant contribution to genetics, and that have the potential to leverage significant funding from other agencies. There are 10 research projects in seven states that into three general classes of endeavor for this fiscal year: "Quality means value", "Biotic Stress Resistance", and "Abiotic Stress Resistance". Barley has unique properties as a human food, as an animal feed, and - of course - as the base of beer. Researchers in Minnesota, Montana, North Dakota, and Wisconsin are leveraging Barley Coordinated Agricultural Project (CAP) funds to systematically characterize the genes, proteins, and metabolic pathways involved in malting quality in contemporary and ancestral barley germplasm. Genetic resistance is the most cost-effective and environmentally sound approach to controlling diseases. By locating and characterizing the genes that confer resistance, and understanding how these genes work, researchers in Minnesota, North Dakota, and Washington are developing tools for resistance breeding that will benefit all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants. Genetic resistance is the most cost-effective and environmentally sound approach to dealing with abiotic stresses. Greater winterhardiness would allow barley acreage to expand into new geographic areas and assure would assure more sustainable production. By locating and characterizing the genes that confer resistance to low temperature stresses, and understanding how these genes work, researchers in Minnesota, Ohio, and Oregon are developing tools for resistance breeding that will benefit all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants.

Project Methods
Barley has unique properties as a human food, as an animal feed, and - of course - as the base of beer. Researchers in Minnesota, Montana, North Dakota, and Wisconsin are leveraging Barley Coordinated Agricultural Project (CAP) funds to systematically characterize the genes, proteins, and metabolic pathways involved in malting quality in contemporary and ancestral barley germplasm. Genetic resistance is the most cost-effective and environmentally sound approach to controlling diseases. By locating and characterizing the genes that confer resistance, and understanding how these genes work, researchers in Minnesota, North Dakota, and Washington are developing tools for resistance breeding that will benefit all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants.Genetic resistance is the most cost-effective and environmentally sound approach to dealing with abiotic stresses. Greater winterhardiness would allow barley acreage to expand into new geographic areas and assure would assure more sustainable production. By locating and characterizing the genes that confer resistance to low temperature stresses, and understanding how these genes work, researchers in Minnesota, Ohio, and Oregon are developing tools for resistance breeding that will benefit all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants.

Progress 08/15/09 to 08/14/11

Outputs
OUTPUTS: This project had tremendous impact on US and international barley science. Virtually every peer-reviewed publication on barley in the past 19 years was based on research supported in some way by this project. Furthermore, this project place the US barley research community in a competitive position to secure the barley CAP and then the Triticeae CAP grants. Barley is a mainstay of American agriculture and it is also an excellent model for genetics research on cereal crops. It is essential to maintain the vigorous US barley research community via competitive funding of targeted genomics research. The US Barley Genome Project (USBGP) is funded by the USDA-CSREES Regional Barley Gene Mapping Special Grant). The USBGP is an inter-disciplinary, multi-institutional endeavor comprised of integrated projects conducted in State Experiment Stations and Federal labs throughout the U.S. Each year, projects are selected for funding that have the potential to make a major impact on U.S. barley production, that promise to make a significant contribution to genetics, and that have the potential to leverage significant funding from other agencies. Barley has unique properties as a human food, as an animal feed, and - of course - as the base of beer. Researchers in Minnesota, Montana, and Wisconsin leveraged Barley CAP funds to systematically characterize the genes, proteins, and metabolic pathways involved in malting quality in contemporary and ancestral barley germplasm. Genetic resistance is the most cost-effective and environmentally sound approach to controlling diseases, insect pests, and dealing with temperature stresses. By locating and characterizing the genes that confer resistance, and understanding how these genes work, researchers in North Dakota, Oregon, and Utah developed tools for resistance breeding have benefited all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants. Progress in plant breeding requires genetic diversity and efficient development of new varieties requires the best of technology. Scientists in all participating states cooperated in developing and applying molecular breeding tools to ensure that useful genes are quickly brought to the barley fields of America. There were two specific tool-development projects - one in Minnesota mined genes from wild barley and the other in Montana developed web-based tools for integrating information on traits that show complex inheritance. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: This research targeted farmers, maltsters, brewers, and consumers and it has led to health, happiness, and prosperity. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The impacts of this project extend from farm to glass and loaf. All barley varieties released in the past 10 years trace to some extent on research supported by this project. The following selected narratives illustrate project impacts. We have identified genes that are differentially expressed in recently-derived germplasm and that exhibit significant correlation to malting quality traits. Both sets of genes are potential targets for selection for enhancing malting quality. Results from this project contribute to our basic understanding of cereal leaf senescence and nitrogen reallocation to developing kernels. Genes identified as functionally important for these processes will be utilized as novel targets in the development of barley varieties with either low (for malting) or high (for food/feed) grain protein concentration. Knowledge gained through this project will also be useful to improve barley N fertilizer use and N harvest index. Results from this project will allow us to efficiently develop cultivars that are resistant to preharvest sprouting (PHS) and have specific quality attributes desired by different end users. These goals will be accomplished using markers developed from this project that can be utilized by plant breeders using molecular marker assisted selection. An example of a cultivar that might be developed using the new markers would be one with high alpha-amylase activity and protein modification during malting but with acceptable PHS resistance. This research confirms that the barley-Pyrenophora teres interaction is complex and involves multiple major host pathogen interactions possibly acting in a gene-for-gene manner. At least three genes involved in pathotype specific resistance/susceptibility are present in the same chromosome 6H region. Closely linked or co-segregating markers will potentially facilitate the introgression of these specific genes into current cultivars via marker assisted selection.A deeper understanding of low temperature tolerance genetics in barley will assist geneticists and breeders of all species. This knowledge can be used to design more efficient and responsive crop improvement strategies. The availability of more winter hardy varieties will benefit producers, processors, and consumers. All will benefit from better stewardship of natural resources afforded by winter habit varieties (notably erosion control, water use efficiency, and genetic diversity) and reduced costs of production. Understanding how plants respond to stress by manipulating flowering time may be exploited to breed crops that are more resistant to stress. Manipulating flowering time may also be useful in non-food crops such as biofuel crops to lengthen vegetative life. It also provides a better basic understanding of plant development and gene regulation.

Publications

• Hayes, P.M. 2011. All publications supported by this research are available via www.barleyworld.org. 4-30-2012.

Progress 08/15/09 to 08/14/10

Outputs
OUTPUTS: The Regional Barley Genome Mapping Special Grant funded the US Barley Genome Project (USBGP). The USBGP was an inter-disciplinary, multi-institutional endeavor comprised of integrated projects conducted in State Experiment Stations and Federal labs throughout the U.S. Each year, projects were selected for funding that had the potential to make a major impact on U.S. barley production, that promised to make a significant contribution to genetics, and that had the potential to leverage significant funding from other agencies. There were 10 research projects in seven states that comprise three general classes of endeavor for this fiscal year: "Quality means value", "Biotic Stress Resistance", and "Abiotic Stress Resistance". Barley has unique properties as a human food, as an animal feed, and - of course - as the base of beer. Researchers in Minnesota, Montana, North Dakota, and Wisconsin leveraged Barley Coordinated Agricultural Project (CAP) funds to systematically characterize the genes, proteins, and metabolic pathways involved in malting quality in contemporary and ancestral barley germplasm. Genetic resistance is the most cost-effective and environmentally sound approach to controlling diseases. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
By locating and characterizing the genes that confer resistance, and understanding how these genes work, researchers in Minnesota, North Dakota, and Washington developed tools for resistance breeding that benefited all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants. Genetic resistance is the most cost-effective and environmentally sound approach to dealing with abiotic stresses. Greater winter hardiness would allow barley acreage to expand into new geographic areas and assure would assure more sustainable production. By locating and characterizing the genes that confer resistance to low temperature stresses, and understanding how these genes work, researchers in Minnesota, Ohio, and Oregon developed tools for resistance breeding that benefited all of American agriculture. Finding and characterizing a gene in barley can provide essential clues for finding similar genes in other crop plants. As a result of this research, Americans now have access to healthier barley-based foods and beverages that promote well-being; farmers have access to more disease resistant crops; and winter food/forage/feed/malt barley has progressed from concept to reality.

Publications

• Szucs, P., V. Blake, P.R. Bhat, S. Chao, T.J. Close, A. Cuesta-Marcos, G.J. Muehlbauer, L. Ramsay, R. Waugh, and P. M. Hayes. 2009. An integrated resource for barley linkage map and malting quality QTL alignment. The Plant Genome. 2:134-140.
• Waugh, R., D. Marshall, B. Thomas, J. Comadran, J. Russell, T. Close, N. Stein, P. Hayes, G. Muehlbauer, J. Cockram, D.Sullivan, I. Mackay, A. Flavell, AGOUEB, BarleyCAP, and L. Ramsay. 2010. Whole-genome association mapping in elite inbred crop varieties. Genome. 59: 967-972.
• Xu, W.W., S. Cho, S.S. Yang, Y-T. Bolon, H. Bilgic, H. Jia, Y. Xiong and G.J. Muehlbauer. 2009. Single-feature polymorphism discovery by computing probe affinity shape powers. BMC Genetics 10:48.
• Zhang, L., Lavery, L., Gill, U., Gill, K., Steffenson, B., Yan, G., Chen, X., and Kleinhofs, A. 2009. A cation/proton-exchanging protein is a candidate for the barley NecS1 gene controlling necrosis and enhanced defense response to stem rust. Theor. Appl. Genet. 118:385-397.
• Brueggeman, R., S. J., and A. Kleinhofs. 2009. The rpg4/Rpg5 stem rust resistance locus in barley; resistance genes and cytoskeleton dynamics. Cell Cycle 8:977-981.
• Close, T.J., P.R. Bhat, S. Lonardi, Y. Wu, N. Rostoks, L. Ramsay, A. Druka, N. Stein, J.T. Svensson, S. Wanamaker, S. Bozdag, M.L. Roose, M.J. Moscou, S. Chao, R. Varshney, P. Szucs, K. Sato, P.M. Hayes, D.E. Matthews, A. Kleinhofs, G.J. Muehlbauer, J. DeYoung, D.F. Marshall, K. Madishetty, R.D. Fenton, P. Condamine, A. Graner, and R. Waugh. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582.
• Condon, F., D.C. Rasmusson1, E. Schiefelbein G. Velasquez, and K.P. Smith. 2009. Effect of Advanced Cycle Breeding on Genetic Gain and Phenotypic Diversity in Barley Breeding Germplasm. Crop Sci. 49: 1751-1761.
• Dabbert, T., R. Okagaki, S. Cho, J. Boddu and G.J. Muehlbauer. 2009. The genetics of barley low-tillering mutants: absent lower laterals (als). Theor. Appl. Genet. 118:1351-1360.
• Filichkin, T.P. , M.A.Vinje, A.D. Budde, A.E. Corey, S.H. Duke, L. Gallagher, J. Helgesson, C.A. Henson, D.E. Obert, J.B. Ohm, S.E. Petrie, A.S. Ross, and P.M. Hayes. 2010. Phenotypic variation for diastatic power,Beta amylase activity, and alpha mylase thermostability vs. allelic variation at the Bmy1 locus in a sample of North American barley germplasm. Crop Sci. 50:826-834.
• Hamblin, M.T., T,J. Close, P.R. Bhat, S. Chao, J.G. Kling, K.J. Abraham, T. Blake, W.S. Brooks, B. Cooper, C.A. Griffey, P.M. Hayes, D.J. Hole, R.D. Horsley, D.E. Obert, K.P. Smith, S.E. Ullrich, G.J. Muehlbauer, and J.L. Jannink. 2010. Population structure and linkage disequilibrium in U.S. barley germplasm: implications for association mapping. Crop Sci. 50:556-566.
• Kongprakhon, P. A. Cuesta-Marcos, P.M. Hayes, K.L. Richardson, P. Sirithunya, K. Sato, B.Steffenson, and T. Toojinda. 2009. Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines. Breeding Sci 59:341-349. Lorang , J., A. Cuesta-Marcos , P. M. Hayes, and T.J. Wolpert. 2010. Identification and mapping of adult-onset sensitivity to victorin in barley. Mol. Breeding. 26:545-550.
• Millett, B. P., Yanwen Xiong, Y., Dahl, Steffenson, B. J., Muehlbauer G. J. 2009. Wild barley accumulates distinct sets of transcripts in response to pathogens of different trophic lifestyles. Physiol. Mol. Plant Pathol. doi:10.1016/j.pmpp.2009.09.006.
• Inostroza, L., A. del Pozo, I. Matus, D. Castillo, P. Hayes, S. Machado and A. Corey. 2009. Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Mol. Breeding. 23:365-376.
• Jannink, J-L., H. Iwata, P.R. Bhat, S. Chao, P. Wenzl, and G.J. Muehlbauer. 2009. Marker imputation in barley association studies. The Plant Genome doi: 10.3835/plantgenome2008.09.2006
• Jia, H., S. Cho and G.J. Muehlbauer. 2009. Transcriptome analysis of a wheat near-isogenic line pair carrying Fusarium head blight resistant and susceptible alleles. Mol. Plant Microbe Interact. 22:1366-1378.
• Kleinhofs, A., Brueggeman, R., Nirmala, J., Zhang, L., Mirlohi, A., Druka, A., Rostoks, N., and Steffenson, B. J. 2009. Barley stem rust resistance genes: structure and function. Plant Genome 2:109-120.
• Munoz-Amatriain, M., L. Cistue, Y. Xiong, H. Bilgic, A.D. Budde, M.R. Schmitt, K.P. Smith, P.M. Hayes and G.J. Muehlbauer. 2009. Structural and functional characterization of a winter malting barley. Theor. Appl. Genet. 120:971-984.
• Olivera, P. D., and Brian J. Steffenson, B. J. 2009. Aegilops sharonensis: Origin, genetics, diversity, and potential for wheat improvement. Botany 87:740-756.
• Rey, J.I., P.M. Hayes, S. E. Petrie, A. Corey, M. Flowers, J.B. Ohm, C. Ong, K. Rhinhart, and A.S. Ross. 2009. Production of dryland barley for human food: quality and agronomic performance. Crop Sci. 49:347-355.
• Schreiber, A.W., T. Sutton, R.A. Caldo, E. Kalashyan, B. Lovell, G. Mayo, G.J. Muehlbauer, A. Druka, R. Waugh, R.P. Wise, P. Langridge and U. Baumann. 2009. Comparative transcriptomics in the Triticeae. BMC Genomics 10:285 doi:10.1186/1471-2164-10-285
• Steffenson, B.J., Jin, Y., Brueggeman, R.S., Kleinhofs, A. and Sun, Y. 2009. Resistance to stem rust race TTKSK maps to the rpg4/Rpg5 complex of chromosome 5H of barley. Phytopathology 99:1135-1141.