Source: UNIV OF MINNESOTA submitted to NRP
BARLEY COORDINATED AGRICULTURAL PROJECT: LEVERAGING GENOMICS, GENETICS AND BREEDING FOR GENE DISCOVERY AND BARLEY IMPROVEMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0219187
Grant No.
2009-85606-05701
Cumulative Award Amt.
(N/A)
Proposal No.
2009-01909
Multistate No.
(N/A)
Project Start Date
Sep 1, 2009
Project End Date
Aug 31, 2011
Grant Year
2009
Program Code
[91710]- Applied Plant Genomics Coordinated Agricultural Project (CAP)
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
Agronomy & Plant Genetics
Non Technical Summary
The barley CAP is a community effort of scientists with expertise ranging from genetics/genomics, breeding, pathology, databases, computer science, food science, and statistics. The overall theme of the barley CAP is to integrate and utilize state-of-the-art genomic tools and approaches in plant breeding programs, thereby facilitating the development of superior barley cultivars. More specifically, we will integrate genetic and trait data to gain access to the genes that control important biological, agronomic, and quality traits. Educational and outreach activities are integrated throughout the project.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20115501080100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1550 - Barley;

Field Of Science
1080 - Genetics;
Goals / Objectives
The overall goal of the barley Coordinated Agricultural Project (CAP) is to integrate genomics tools into barley breeding to enhance the efficiency and effectiveness of barley improvement. There are five objectives: (1) develop an integrated 3,000 single nucleotide polymorphism (SNP)-based genetic/physical/expression map of the barley genome; (2) develop an integrated web portal and database for efficient access to map, gene expression, and trait data; (3) access economically important genes using association genetics and diverse breeding germplasm; (4) develop elite barley germplasm using high-throughput marker-assisted selection; and (5) educate students, scientists, farmers, and processors in the use of genomics technology for gene discovery and crop improvement. The expected outputs are: (1) a SNP map integrated with expression data and the BAC-based physical map; (2) a database that contains pedigree, trait, and SNP data from U.S. barley breeding programs, and SNP maps that are integrated with gene expression datasets and the physical map; (3) haplotype structure and linkage disequilibrium estimates of U.S. barley breeding lines; (4) identification of marker-trait associations; (5) initiation of marker-assisted selection within breeding programs; (6) education of students and breeders on association mapping and marker-assisted selection; and (7) enhanced linkages with and extension programming for barley growers, extension educators, and industry personnel.
Project Methods
Approximately 3,000 mapped SNPs will be integrated with the emerging BAC-based physical map and Barley1 GeneChip expression data. We will use the SNP markers to genotype 960 lines from ten barley-breeding programs. Trait data for over 40 traits will be determined for these same 960 lines. The SNP genotyping will also be used to understand linkage disequilibrium and the haplotype blocks in current barley breeding germplasm. The genotype and trait data will be combined to conduct association genetics-based studies to detect marker-trait associations. Detecting marker-trait associations using breeding germplasm will lead directly to the implementation of marker-assisted selection (MAS) to manipulate important traits and develop improved varieties. The project database "The Hordeum Toolbox" will contain all trait and SNP data compiled by the project and the database will also host the barley genetic maps, physical map and expression databases. The project will host a workshop for students and breeders on marker-assisted selection and association genetics. The project has also organized extension teams in North Dakota, Montana and Idaho. These teams will host a set of barley days that will provide important information to growers on future barley production research. The project will also develop technical information on molecular breeding for students and breeders, and nontechnical information on barley for the general public. This information will be placed on the eXtension website.

Progress 09/01/09 to 08/31/11

Outputs
OUTPUTS: There were five objectives: (1) develop an integrated 3,000 single nucleotide polymorphism (SNP)-based genetic/physical/expression map of the barley genome; (2) develop an integrated web portal and database for efficient access to map, gene expression, and trait data; (3) access economically important genes using association genetics and diverse breeding germplasm; (4) develop elite barley germplasm using high-throughput marker-assisted selection; and (5) educate students, scientists, farmers, processors, and consumers in use of genomics technology for gene discovery and crop improvement. A set of 3,072 SNPs (BarleyOPA1 and BarleyOPA2) was developed as an international genotyping platform. A SNP map of 2,943 SNPs was developed and refinement of the map was completed that resulted in 2,994 SNP markers mapped with increased resolution. The SNPs were integrated with the physical map as part of the international collaboration to sequence the barley genome. The database "The Hordeum Toolbox" (http://www.hordeumtoolbox.org) was developed and is being used by the oat community (The Avena Toolbox; http://avena.pw.usda.gov/tat/) and was adopted by the Triticeae Coordinated Agricultural Project (The Triticeae Toolbox; http://triticeaetoolbox.org/) Each of the participating ten breeding programs in the barley CAP submitted 96 breeding lines in the four years of the project, for a total of 3,840 lines. These lines were genotyped with BOPA1 and BOPA2 SNPs, and phenotyped for approximately 30 traits including: malting quality, agronomic performance, disease resistance, and food quality. Quantitative trait loci (QTL) were identified for Fusarium head blight resistance, resistance to deoxynivalenol accumulation, spot blotch resistance, Ug99 resistance, common root rot resistance, Septoria Speckled Leaf Blotch resistance, preharvest sprouting, heading date, yield, malting quality traits and winter hardiness. Based on the QTL mapping results, SNP genotyping platforms were developed to implement marker-assisted selection and genomic selection strategies within breeding programs. The project website (www.barleycap.org) was frequently updated and 14 newsletters describing the progress of the project were produced and distributed. We collaborated with the Institute of Barley Malt Sciences (http://www.ag.ndsu.edu/ibms/; Fargo, ND) to host grower meetings, develop outreach materials and deliver information to growers. Five factsheets were developed for and a podcast on the stem rust pathogen Ug99 was developed and provided to growers and industry personnel. Numerous presentations were given on the project to grower groups, industry representatives and scientific groups. We hosted two workshops on association mapping, marker-assisted selection and genomic selection, and a one-day association mapping analysis session. We worked with the Solanaceae CAP to develop a barley grower page on the eXtension website (http://www.extension.org/). PARTICIPANTS: Byung-Kee Baik, Washington State University; Rex Bernardo, University of Minnesota; Tom Blake, Montana State University; Peter Bradbury, USDA-ARS, Ithaca, NY; Victoria Carollo, Montana State University; Shiaoman Chao, USDA-ARS, Fargo, ND; Timothy Close, UC, Riverside; Blake Cooper, Busch Agricultural Research Inc.; Julie Dickerson, Iowa State University; Ruth Dill-Macky, University of Minnesota; Carl Griffey, Virginia Tech; Patrick Hayes, Oregon State University; David Hole, Utah State University; Richard Horsley, North Dakota State University; Lee Jackson, UC, Davis; Jean-Luc Jannink, USDA-ARS, Ithaca, NY; Jennifer Kling, Oregon State University; Peggy Lemaux, UC, Berkeley; Stefano Lonardi, UC, Riverside; David Matthews, USDA-ARS, Ithaca, NY; Stephen Neate, North Dakota State University; Donald Obert, USDA-ARS, Aberdeen, ID; Mark Schmitt, USDA-ARS, Madison, WI; Paul Schwarz, North Dakota State University; Kevin Smith, University of Minnesota; Brian Steffenson, University of Minnesota; Steven Ullrich, Washington State University; Mitch Wise, USDA-ARS, Madison, WI; Roger Wise, USDA-ARS, Ames, IA TARGET AUDIENCES: Breeders, geneticists, students, growers, industry personnel PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The SNP map was used by the international barley community for various genetic and breeding studies. 3,840 breeding lines from ten breeding programs have been evaluated for numerous traits and genotyped with 3,072 BOPA1 and BOPA2 SNPs. The Hordeum Toolbox database is fully functional and was adopted by the oat and wheat breeding communities. QTL have been detected for a variety of traits and the marker-assisted and genomic selection is being implemented based on the QTL mapping results. Barley CAP participants (PIs, graduate students and postdocs) have been trained in handling large SNP and phenotype datasets and conducting association mapping. The extension teams have delivered information to barley growers on varieties and agronomic issues.

Publications

  • Wang, H., K.P. Smith, E. Combs, T. Blake, R. Horsley and G.J. Muehlbauer. 2011. Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor. Appl. Genet. 124:111-124.
  • von Zitzewitz, J., F. Condon, A. Corey, A. Cuesta‐Marcos, T.Filichkina, K. Haggard, S.P. Fisk, K.P. Smith, G.J. Muehlbauer, I. Karsai and P.M. Hayes. 2011. The genetics of winterhardiness in barley: perspectives from genome‐wide association mapping. The Plant Genome 4:76-91.
  • Sato, K., T.J. Close, P. Bhat, M. Munoz-Amatriain and G.J. Muehlbauer. 2011. Genetic mapping and alignment of recombinant chromosome substitution lines from a cross of EST donors by SNP typing in barley. Plant and Cell Physiology 52:728-737.
  • Ramsay, L., J. Comadran, A. Druka, D.F. Marshall, W.T.B. Thomas, M. Macaulay, K. MacKenzie, C. Simpson, J. Fuller, N. Bonar, P.M. Hayes, U. Lunqvist, J.D. Franckowiak, T.J. Close, G.J. Muehlbauer and R. Waugh. 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nature Genetics 43:169-172.
  • Sato, K., T.J. Close, P. Bhat, M. Munoz-Amatriain and G.J. Muehlbauer. 2011. Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley. Plant and Cell Physiology 52:728-737.
  • Chutimanitsakun, Y., R.W. Nipper, A. Cuesta-Marcos, E.A. Johnson, and P.M. Hayes. 2011. Construction and application of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12:4.
  • Nair, S., M. Knoblauch, S.E. Ullrich, and B.-K. Baik. 2011. Microstructure of hard and soft kernels of barley. J. Cereal Sci. 54:354-362.
  • Wu, Y., P. Bhat, T.J. Close and S. Lonardi. Efficient and accurate construction of genetic linkage maps from noisy and missing genotyping data. R. Giancarlo and S. Hannenhalli (Eds.): WABI 2007, LNBI 4645, pp. 395-406. Springer-Verlag Berlin Hedelberg. http://www.cs.ucr.edu/~stelo/papers/WABI07.pdf
  • Schwarz, P., R. Horsley, and K. Hertsgaard. 2008. Survey of barley producers in Idaho, Montana and North Dakota. Master Brewers Association of the Americas Technical Quarterly 45:99-107.
  • Wu, Y., P.R. Bhat, Timothy J. Close and Stefano Lonardi. 2008. Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genetics 4:e1000212.
  • 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 2:11-22.
  • Waugh, R., Jannink, J-L., G.J. Muehlbauer, and L. Ramsay. 2009. The emergence of whole genome association scans in barley. Curr. Opin. Plant Biol. 12:218-222.
  • Bozdag, S., T.J. Close, and S. Lonardi. 2009. A compartmentalized approach to the assembly of physical maps. BMC Bioinformatics. 10: p.217.
  • Szucs, P., V.C. Blake, P.R. Bhat, T.J. Close, G. 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.
  • Heffner, E.L., M.E. Sorrells, and J.-L. Jannink. 2009. Genomic selection for crop improvement. Crop Sci. 49:1-12.
  • Zhong, S., J.C.M. Dekkers, R.L. Fernando, and J.L. Jannink. 2009. Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355-364.
  • 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.
  • 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. 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.
  • Massman, J., B. Cooper, R. Horsley, P. Schwarz, Y. Dong, S. Neate, R. Dill-Macky, J. Franckowiak, G. Muehlbauer S. Chao, and K. Smith. 2011. Association mapping of Fusarium head blight resistance QTL in contemporary barley breeding germplasm. Mol. Breed. 27:439-454.
  • Brooks, W. S. M. E. Vaughn, C. A. Griffey, W. E. Thomason, J. J. Paling, R. M. Pitman, D. W. Dunaway, R. A. Corbin, J. C. Kenner, E. G. Hokanson, H. D. Behl, B. R. Beahm, S. Y. Liu, P. G. Gundrum, A. M. Price, D. E. Brann, D. L. Whitt, J. T. Custis, D. E. Starner, S. A. Gulick, S. R. Ashburn, E. H. Jones Jr., D. S. Marshall, M. O. Fountain, T. D. Tuong, D. P. Livingston, R. Premakumar, M. J. Kurantz, F. Taylor, R. A. Moreau, and K. B. Hicks. 2011. Registration of 'Dan' Winter Hulless Barley. J. Plant Reg. 5: 1-4.
  • O'Boyle, P. D., W. S. Brooks, B. J. Steffenson, E.L Stromberg, and C. A. Griffey. 2011. Genetic characterization of barley net blotch resistance genes. Plant Disease 95:19-23.
  • Verhoeven, E. C., M. Bonman, P. Bregitzer, B. Brunick, B. Cooper, A.E. Corey, A. Cuesta-Marcos, T. Filichkina, C.C. Mundt, D. Obert, B. Rossnagel, K. Richardson, and P.M. Hayes. 2011. Registration of the BISON genetic stocks in Hordeum vulgare L. J. Plant Reg. 5:135-140.
  • Comadran, J., L. Ramsay, K. MacKenzie, P. Hayes, T.J. Close, G. Muehlbauer, N. Stein and R. Waugh. 2011. Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor. Appl. Genet. 122:523-531.
  • Bradbury, P.J., T. Parker, M.T. Hamblin, and J.-L. Jannink. 2011. Assessment of power and false discovery in genome-wide association studies using the BarleyCAP germplasm. Crop Sci. 51:52-59.
  • Nair, S., Ullrich, S. E., and Baik, B.-K. 2011. Association of barley kernel hardness with physical grain traits and food processing parameters. Cereal Chem. 88:147-152.
  • Lorenz, A. J., S. Chao, F.G. Asoro, E.L. Heffner, T. Hayashi, H. Iwata, K.P. Smith, M.E. Sorrells and J-L. Jannink. 2011. Genomic Selection in Plant Breeding: Knowledge and Prospects. Advances in Agronomy 110:77-123.
  • Hamblin, M.T., E.S. Buckler, and J.-L. Jannink. 2011. Population genetics of genomics-based crop improvement methods. Trends in Genetics 27:98-106.
  • Hamblin, M.T., and J.-L. Jannink. 2011. Factors affecting the power of haplotype markers in association studies. Plant Gen. 4:145-153.
  • Iwata, H., and J.-L. Jannink. 2011. Accuracy of genomic selection prediction in barley breeding programs: a simulation study based on the real single nucleotide polymorphism data of barley breeding lines. Crop Science 51:1915-1927.
  • Heffner, E.L., J.-L. Jannink, H. Iwata, E. Souza, and M.E. Sorrells. 2011. Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Science 51:2597-2606.
  • Heffner, E.L., J.-L. Jannink, and M.E. Sorrells. 2011. Genomic selection accuracy using multifamily prediction models in a wheat breeding program. The Plant Genome 4:65-75.
  • Elshire R.J., J.C. Glaubitz, Q. Sun, J.A. Poland, K. Kawamoto, E.S. Buckler, and S.E. Mitchell. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379.
  • Munoz-Amatriain, M., M.J. Moscou, P.R. Bhat, J.T. Svensson, J. Bartos, P. Suchankova, H. Simkova, T.R. Endo, R.D. Fenton, S. Lonardi, A.M. Castillo, S. Chao, L. Cistue, A. Cuesta-Marcos, K.L. Forrest, M.J. Hayden, P.M. Hayes, R.D. Horsley, K. Makoto, D. Moody, K. Sato, M.P. Valles, B.B.H. Wulff, G.J. Muehlbauer, J. Dolezel and T.J. Close. 2011. An improved consensus linkage map of barley based on flow sorted chromosomes and SNP markers. The Plant Genome 4:238-249.
  • Gutierrez L., A. Cuesta-Marcos, A. J. Castro, J. von Zitzewitz, P. M. Hayes. 2011. Association mapping of malting quality quantitative trait loci in winter barley: positive signals from small germplasm arrays. The Plant Genome 4:256-272.
  • Poland, J.A., P.J. Brown, M.E. Sorrells, J-L. Jannink. 2011. Development of high-density genetics maps for barley and wheat using genotyping-by-sequencing. PLoS One 10.1371/journal.pone.0032253.
  • Thomas, W.T.B., P.M. Hayes, and L.S. Dahleen. Application of molecular genetics and transformation to barley improvement. 2011. In: Barley: Production, Improvement, and Uses. S.E. Ullrich (ed.) Wiley-Blackwell
  • Liang, M., D. Hole, J. Wu, T. Blake, and Y. Wu. 2012. Expression and functional analysis of NUCLEAR FACTOR-Y, subunit B genes in barley. Planta 235:779-791.
  • Blake, V.C., J.G. Kling, P.M. Hayes, J.-L. Jannink, S.R. Jillella, J. Lee, D.E. Matthews, S. Chao, T.J. Close, G.J. Muehlbauer, K.P. Smith, R.P. Wise and J.A. Dickerson. 2012. The Hordeum Toolbox - The barley coordinated agricultural project genotype and phenotype resource. The Plant Genome 5:81-91. [Cover Article]
  • Zhou, H., G. Muehlbauer and B.J. Steffenson. 2012. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J. Zhejiang Univ. 13:438-451.
  • Lorenz, A.J., K.P. Smith, and J.-L. Jannink. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci. Vol. 52:1609-1621.
  • The International Barley Sequencing Consortium. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature doi:10.1038/nature11543.
  • Berger, G.L., S. Liu, M.D. Hall, W.S. Brooks, S. Chao, G.J. Muehlbauer, B.-K. Baik, and C.A. Griffey. 2011. Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping. Theor. Appl. Genet. DOI: 10.1007/s00122-012-2011-7
  • Fisk, S.P., A. Cuesta-Marcos, L. Cistue, J. Russell, K.P. Smith, P.S. Baenziger, Z. Bedo, A. Corey, T. Filichkin, I. Karsai, R. Waugh and P.M. Hayes. 2012. FR-H3: A new QTL to assist in the development of fall-sown barley with superior low temperature tolerance. Theor. Appl. Genet. DOI 10.1007/s00122-012-1982-8
  • Chao, S. and C. Lawley. 2012. Use of GoldenGate assay for SNP genotyping in cereal crops. Submitted to Methods in Molecular Biology series on Plant Genotyping, Humana Press, USA
  • Li, Y. and P.B. Schwarz. 2012. Use of ferrous oxidation-xylenol orange (FOX) assay to determine lipoxygenase activity in barley and malt. J. Am. Soc. Brew. Chem. In press.
  • Variety releases: Verdant (2011), Alba (2012), Rasmusson (2010)
  • Hayes, P. and P. Szucs. 2006. Disequilibrium and association in barley: thinking outside the glass. Proc. Natl. Acad Sci. USA 103:18385-18386.
  • Bozdag, S., T.J. Close and S. Lonardi. 2007. A compartmentalized approach to the assembly of physical maps. Proceedings of BIBE 2007-IEEE International Symposium on Bioinformatics & Bioengineering, pp. 218-225, Boston, MA.
  • Wu, Y., P. Bhat, T.J. Close and S. Lonardi. 2007. Efficient and accurate construction of genetic linkage maps from noisy and missing genotyping data. Proceedings of WABI 2007 - Workshop on Algorithms in Bioinformatics, LNBI 4645, pp.395-406, Philadelphia PA.
  • Wu, Y., L. Liu, T.J. Close and S. Lonardi. 2007. Deconvoluting the BAC-gene relationships using a physical map. Proceedings of CSB 2007 - Computational Systems Bioinformatics Conference, pp. 203-214, San Diego, CA.
  • Bozdag, S., T.J. Close, and S. Lonardi. 2008 Computing the minimal tiling path from a physical map by integer linear programming. K.A. Crandall and J. Lagergren (Eds.): WABI 2008, LNBI 5251, pp. 148-161. Springer-Verlag Berlin Hedelberg. http://www.cs.ucr.edu/~stelo/papers/WABI08.pdf
  • Wu, Y., T.J. Close, and S. Lonardi. 2008. On the accurate construction of consensus genetic maps. http://www.cs.ucr.edu/~stelo/papers/CSB08.pdf
  • Wu, Y., L. Liu, T.J. Close and S. Lonardi. 2008. Deconvoluting BAC-gene relationships using a physical map. Journal of Bioinformatics and Computational Biology. 6:603-622.
http://www.cs.ucr.edu/~stelo/papers/jbcb08.pdf
  • 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.
  • Griffey, C., W. Brooks, M. Kurantz, W. Thomason, F. Taylor, D. Obert, R. Moreau, R. Flores, M. Sohn, and K. Hicks. 2009. Grain composition of Virginia winter barley and implications for use in feed, food, and biofuels production. J. Cereal Chemistry 51:41-49.
  • Hamblin, M.T., T.J. Close, P.R. Bhat, S. Chao, 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 US barley germplasm: implications for association mapping. Crop Sci. 50:556-566.
  • Bernardo, R. 2010. Genome wide selection with minimal crossing in a self-pollinated crop. Crop Sci. 50:624-627.
  • Roy, J.K., K.P. Smith, G.J. Muehlbauer, S. Chao, T.J. Close, and B.J. Steffenson. 2010. Association mapping of spot blotch resistance in wild barley. Mol. Breed. 26:243-256.
  • Iwata, H., and J.-L. Jannink. 2010. Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines. Crop Sci. 50:1269-1278.
  • Nair, S., S.E. Ullrich, T.K. Blake, B. Cooper, C.A. Griffey, P.M. Hayes, D.J. Hole, R.D. Horsley, D.E. Obert, K.P. Smith, G.J. Muehlbauer, and B.-K. Baik. 2010. Variation in kernel hardness and associated traits in U.S. barley breeding lines. Cereal Chem. 87:461-466.
  • Jannink, J.-L., A.J. Lorenz and H. Iwata. 2010. Genomic selection in plant breeding: from theory to practice. Brief. Function. Genomics Proteomics 9:166-177.
  • Heffner, E. L., A.J. Lorenz, J.-L. Jannink and M.E. Sorrells. 2010. Plant breeding with genomic selection: potential gain per unit time and cost. Crop Sci. 50:1681-1690.
  • Jannink, J.-L. 2010. Dynamics of long-term genomic selection. Genet. Sel. Evol. 42:35.

  • Jannink, J.-L., A.J. Lorenz, and H. Iwata. 2010. Genomic selection in plant breeding: from theory to practice. Brief. Funct. Genom. Proteom. 9:166-177.
  • Waugh, R., D. Marshall, B. Thomas, J. Comadran, J. Russell, T. Close, N. Stein, P. Hayes, G. Muehlbauer, J. Cockram, D. O'Sullivan, I. Mackay, A. Flavell, AGOUEB, BarleyCAP, and L. Ramsay. 2010. Whole-genome association mapping in elite inbred crop varieties. Genome 53:967-972.
  • Cuesta-Marcos, A., P. Szucs, T.J. Close, T. Filichkin, G.J. Muehlbauer, K.P. Smith and P.M. Hayes. 2010. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 11:707.
  • Lorenz, A.J., M.T. Hamblin, and J.-L. Jannink. 2010. Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley. PLoS ONE 5(11): e14079.
  • Munoz-Amatriain, M., Y. Xiong, H. Bilgic, A.D. Budde, M.R. Schmitt, K.P. Smith, and G.J. Muehlbauer. 2010. Transcriptome analysis of a breeding program pedigree examines gene expression diversity and reveals target genes for the improvement of malting quality. BMC Genomics 11:653.
  • Cistue, L., S. Chao, Y. Chutimanitsakun, A. Corey, A. Cuesta-Marcos, B. Echavarri , T. Filichkina, N. Garcia-Marino, I. Romagosa, and P.M. Hayes. 2010. Comparative mapping of the Oregon Wolfe Barley using doubled haploid lines derived from female and male gametes. Theor. Appl Genet. 122:1399-1410.
  • Smith, K.P., D.C. Rasmusson, E. Schiefelbein, J.J. Wiersma, J.V. Wiersma, A. Budde, R. Dill-Macky, and B. Steffenson. 2010. Registration of 'Rasmusson' barley. Journal of Plant Registrations 4:167-170.
  • Ramsay, L., J. Comadran, A. Druka, D.F. Marshall, W.T.B. Thomas, M. Macaulay, K. MacKenzie, C. Simpson, J. Fuller, A. Roberts, P.M. Hayes, U. Lunqvist, J.D. Franckowiak, T.J. Close, G.J. Muehlbauer and R. Waugh. 2011. Parallel selection at orthologous loci during the domestication of the grasses. Nature Genetics 43:169-172.


Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: There are five objectives: (1) develop an integrated 3,000 single nucleotide polymorphism (SNP)-based genetic/physical/expression map of the barley genome; (2) develop an integrated web portal and database for efficient access to map, gene expression, and trait data; (3) access economically important genes using association genetics and diverse breeding germplasm; (4) develop elite barley germplasm using high-throughput marker-assisted selection; and (5) educate students, scientists, farmers, processors, and consumers in use of genomics technology for gene discovery and crop improvement. A set of 3,072 SNPs (BarleyOPA1 and BarleyOPA2), have been developed as an international genotyping platform. A SNP map of 2,943 SNPs was developed and refinement of the map is in process. A total of 1,960 BOPA1 and BOPA2 SNPs have been anchored directly to 2,522 gene-bearing Morex BACs. Integrating these 2,522 BACs with 83,831 fingerprinted BACs anchored approximately 20,000 gene-bearing Morex BACs to the genetic map. The database "The Hordeum Toolbox" (http://www.hordeumtoolbox.org) to house the data from the project is fully functional and is housed at GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml). The oat and wheat breeding communities are adopting the THT database. Each of the participating ten breeding programs have submitted 96 breeding lines in the four years of the project, for a total of 3,840 lines. These lines have been genotyped with BOPA1 and BOPA2, and phenotyped for approximately 30 traits including: malting quality, agronomic performance, disease resistance, and food quality. Quantitative trait loci (QTL) have been identified for Fusarium head blight resistance, resistance to deoxynivalenol accumulation, spot blotch resistance, Ug99 resistance, common root rot resistance, preharvest sprouting, heading date, yield, malting quality traits and winter hardiness. Based on the QTL mapping results, SNP genotyping platforms have been developed to implement marker-assisted selection strategies within breeding programs. The project website (www.barleycap.org) has been frequently updated and three newsletters describing the progress of the project were produced and distributed. We collaborated with the Institute of Barley Malt Sciences (http://www.ag.ndsu.edu/ibms/; Fargo, ND) to host grower meetings, develop outreach materials and deliver information to growers. A factsheet and podcast on the stem rust pathogen Ug99 have been developed and provided to growers and industry personnel. Numerous presentations have been given on the project to grower groups, industry representatives and scientific groups. We hosted a one-day association mapping analysis session with project participants. We worked with the Solanaceae CAP to develop a barley grower page on the eXtension website (http://www.extension.org/). PARTICIPANTS: Byung-Kee Baik, Washington State University; Rex Bernardo, University of Minnesota; Tom Blake, Montana State University; Peter Bradbury, USDA-ARS, Ithaca, NY; Victoria Carollo, Montana State University; Shiaoman Chao, USDA-ARS, Fargo, ND; Timothy Close, UC, Riverside; Blake Cooper, Busch Agricultural Research Inc.; Julie Dickerson, Iowa State University; Ruth Dill-Macky, University of Minnesota; Carl Griffey, Virginia Tech; Patrick Hayes, Oregon State University; David Hole, Utah State University; Richard Horsley, North Dakota State University; Lee Jackson, UC, Davis; Jean-Luc Jannink, USDA-ARS, Ithaca, NY; Jennifer Kling, Oregon State University; Peggy Lemaux, UC, Berkeley; Stefano Lonardi, UC, Riverside; David Matthews, USDA-ARS, Ithaca, NY; Stephen Neate, North Dakota State University; Donald Obert, USDA-ARS, Aberdeen, ID; Mark Schmitt, USDA-ARS, Madison, WI; Paul Schwarz, North Dakota State University; Kevin Smith, University of Minnesota; Brian Steffenson, University of Minnesota; Steven Ullrich, Washington State University; Mitch Wise, USDA-ARS, Madison, WI; Roger Wise, USDA-ARS, Ames, IA TARGET AUDIENCES: Breeders, geneticists, students, growers, industry personnel PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
The SNP map is being used by the international barley community for various genetic and breeding studies. 3,840 breeding lines from ten breeding programs have been evaluated for numerous traits and genotyped with 3,072 BOPA1 and BOPA2 SNPs. The Hordeum Toolbox database is fully functional and has been adopted by the oat and wheat breeding communities. QTL have been detected for a variety of traits and the marker-assisted selection is being implemented based on the QTL mapping results. Barley CAP participants have been trained in handling large SNP and phenotype datasets and conducting association mapping. The extension teams have delivered information to barley growers on varieties and agronomic issues.

Publications

  • 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.
  • 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. 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.
  • 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.
  • Hamblin, M.T., T.J. Close, P.R. Bhat, S. Chao, 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 US barley germplasm: implications for association mapping. Crop Sci. 50:556-566.
  • Bernardo, R. 2010. Genome wide selection with minimal crossing in a self-pollinated crop. Crop Sci. 50:624-627.
  • Massman, J., B. Cooper, R. Horsley, P. Schwarz, Y. Dong, S. Neate, R. Dill-Macky, J. Franckowiak, G. Muehlbauer S. Chao, and K. Smith. 2010. Association mapping of Fusarium head blight resistance QTL in contemporary barley breeding germplasm. Mol. Breed. DOI: 10.1007/s11032-010-9442-0.
  • Roy, J.K., K.P. Smith, G.J. Muehlbauer, S. Chao, T.J. Close, and B.J. Steffenson. 2010. Association mapping of spot blotch resistance in wild barley. Mol. Breed. 26:243-256.
  • Iwata, H., and J.-L. Jannink. 2010. Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines. Crop Sci. 50:1269-1278.
  • Nair, S., S.E. Ullrich, T.K. Blake, B. Cooper, C.A. Griffey, P.M. Hayes, D.J. Hole, R.D. Horsley, D.E. Obert, K.P. Smith, G.J. Muehlbauer, and B.-K. Baik. 2010. Variation in kernel hardness and associated traits in U.S. barley breeding lines. Cereal Chem. 87:461-466.
  • Jannink, J.-L., A.J. Lorenz and H. Iwata. 2010. Genomic selection in plant breeding: from theory to practice. Brief. Function. Genomics Proteomics 9:166-177.
  • Heffner, E. L., A.J. Lorenz, J.-L. Jannink and M.E. Sorrells. 2010. Plant breeding with genomic selection: potential gain per unit time and cost. Crop Sci. 50:1681-1690.
  • Jannink, J.-L. 2010. Dynamics of long-term genomic selection. Genet. Sel. Evol. 42:35.
  • Jannink, J.-L., A.J. Lorenz, and H. Iwata. 2010. Genomic selection in plant breeding: from theory to practice. Brief. Funct. Genom. Proteom. 9:166-177.
  • Waugh, R., D. Marshall, B. Thomas, J. Comadran, J. Russell, T. Close, N. Stein, P. Hayes, G. Muehlbauer, J. Cockram, D. O'Sullivan, I. Mackay, A. Flavell, AGOUEB, BarleyCAP, and L. Ramsay. 2010. Whole-genome association mapping in elite inbred crop varieties. Genome 53:967-972.
  • Griffey, C., W. Brooks, M. Kurantz, W. Thomason, F. Taylor, D. Obert, R. Moreau, R. Flores, M. Sohn, and K. Hicks. 2009. Grain composition of Virginia winter barley and implications for use in feed, food, and biofuels production. J. Cereal Chemistry 51:41-49.