Table of Contents
International Journal of Plant Genomics
Volume 2008 (2008), Article ID 486258, 13 pages
http://dx.doi.org/10.1155/2008/486258
Review Article

Barley Genomics: An Overview

Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstraße 3, 06466 Gatersleben, Germany

Received 15 November 2007; Accepted 8 February 2008

Academic Editor: P. Gupta

Copyright © 2008 Nese Sreenivasulu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. F. Salamini, H. Özkan, A. Brandolini, R. Schäfer-Pregl, and W. Martin, “Genetics and geography of wild cereal domestication in the near east,” Nature Reviews Genetics, vol. 3, no. 6, pp. 429–441, 2002. View at Google Scholar
  2. W. H. Schuster, “Welchen Beitrag leistet die Pflanzenzüchtung zurLeistungssteigerung von Kulturpflanzenarten,” Pflanzenbauwissenschaften, vol. 1, pp. 9–18, 1997. View at Google Scholar
  3. A. Rafalski, “Applications of single nucleotide polymorphisms in crop genetics,” Current Opinion in Plant Biology, vol. 5, no. 2, pp. 94–100, 2002. View at Publisher · View at Google Scholar
  4. R. K. Varshney, D. A. Hoisington, and A. K. Tyagi, “Advances in cereal genomics and applications in crop breeding,” Trends in Biotechnology, vol. 24, no. 11, pp. 490–499, 2006. View at Publisher · View at Google Scholar
  5. U. Wobus and N. Sreenivasulu, “Genomics approaches for the improvement of cereals,” in European Training and Networking Activity, Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond—A Course Book, J. Freitag, Ed., pp. 146–155, National Institute of Biology, Ljubljana Slovenia, 2006. View at Google Scholar
  6. M. Bagge, X. Xia, and T. Lübberstedt, “Functional markers in wheat,” Current Opinion in Plant Biology, vol. 10, no. 2, pp. 211–216, 2007. View at Publisher · View at Google Scholar
  7. A. S. Milligan, S. Lopato, and P. Langridge, “Functional genomics of seed development in cereals,” in Cereal Genomics, K. P. Gupta and R. K. Varshney, Eds., pp. 447–481, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2004. View at Google Scholar
  8. R. K. Varshney, P. Langridge, and A. Graner, “Application of genomics to molecular breeding of wheat and barley,” Advances of Genetics, vol. 58, pp. 121–155, 2007. View at Google Scholar
  9. H. Zhang, N. Sreenivasulu, W. Weschke et al., “Large-scale analysis of the barley transcriptome based on expressed sequence tags,” The Plant Journal, vol. 40, no. 2, pp. 276–290, 2004. View at Publisher · View at Google Scholar
  10. A. Druka, G. Muehlbauer, I. Druka et al., “An atlas of gene expression from seed to seed through barley development,” Functional & Integrative Genomics, vol. 6, no. 3, pp. 202–211, 2006. View at Publisher · View at Google Scholar
  11. N. Sreenivasulu, V. Radchuk, M. Strickert, O. Miersch, W. Weschke, and U. Wobus, “Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA- regulated maturation in developing barley seeds,” The Plant Journal, vol. 47, no. 2, pp. 310–327, 2006. View at Publisher · View at Google Scholar
  12. N. Rostoks, S. Mudie, L. Cardle et al., “Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress,” Molecular Genetics and Genomics, vol. 274, no. 5, pp. 515–527, 2005. View at Publisher · View at Google Scholar
  13. P. R. Hearnden, P. J. Eckermann, G. L. McMichael, M. J. Hayden, J. K. Eglinton, and K. J. Chalmers, “A genetic map of 1,000 SSR and DArT markers in a wide barley cross,” Theoretical and Applied Genetics, vol. 115, no. 3, pp. 383–391, 2007. View at Publisher · View at Google Scholar
  14. N. Stein, M. Prasad, U. Scholz et al., “A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics,” Theoretical and Applied Genetics, vol. 114, no. 5, pp. 823–839, 2007. View at Publisher · View at Google Scholar
  15. A. K. M. R. Islam, K. W. Shepherd, and D. H. B. Sparrow, “Isolation and characterization of euplasmic wheat-barley chromosome addition lines,” Heredity, vol. 46, pp. 161–174, 1981. View at Google Scholar
  16. S. Cho, D. F. Garvin, and G. J. Muehlbauer, “Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines,” Genetics, vol. 172, no. 2, pp. 1277–1285, 2006. View at Publisher · View at Google Scholar
  17. G. Künzel, L. Korzun, and A. Meister, “Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints,” Genetics, vol. 154, no. 1, pp. 397–412, 2000. View at Google Scholar
  18. A. Masoudi-Nejad, S. Nasuda, M.-T. Bihoreau, R. Waugh, and T. R. Endo, “An alternative to radiation hybrid mapping for large-scale genome analysis in barley,” Molecular Genetics and Genomics, vol. 274, no. 6, pp. 589–594, 2005. View at Publisher · View at Google Scholar
  19. Y. Yu, J. P. Tomkins, R. Waugh et al., “A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes,” Theoretical and Applied Genetics, vol. 101, no. 7, pp. 1093–1099, 2000. View at Publisher · View at Google Scholar
  20. E. Isidore, B. Scherrer, A. Bellec et al., “Direct targeting and rapid isolation of BAC clones spanning a defined chromosome region,” Functional & Integrative Genomics, vol. 5, no. 2, pp. 97–103, 2005. View at Publisher · View at Google Scholar
  21. J. L. Stephens, S. E. Brown, N. L. V. Lapitan, and D. L. Knudson, “Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique,” Genome, vol. 47, no. 1, pp. 179–189, 2004. View at Publisher · View at Google Scholar
  22. R. K. Varshney, I. Grosse, U. Hähnel et al., “Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome,” Theoretical and Applied Genetics, vol. 113, no. 2, pp. 239–250, 2006. View at Publisher · View at Google Scholar
  23. N. Stein, “Triticeae genomics: advances in sequence analysis of large genome cereal crops,” Chromosome Research, vol. 15, no. 1, pp. 21–31, 2007. View at Publisher · View at Google Scholar
  24. K. Madishetty, P. Condamine, J. T. Svensson, E. Rodriguez, and T. J. Close, “An improved method to identify BAC clones using pooled overgos,” Nucleic Acids Research, vol. 35, no. 1, p. e5, 2007. View at Publisher · View at Google Scholar
  25. N. Sreenivasulu, L. Altschmied, V. Radchuk, S. Gubatz, U. Wobus, and W. Weschke, “Transcript profiles and deduced changes of metabolic pathways in maternal and filial tissues of developing barley grains,” The Plant Journal, vol. 37, no. 4, pp. 539–553, 2004. View at Publisher · View at Google Scholar
  26. Z. N. Ozturk, V. Talamé, M. Deyholos et al., “Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley,” Plant Molecular Biology, vol. 48, no. 5-6, pp. 551–573, 2002. View at Publisher · View at Google Scholar
  27. T. J. Close, S. I. Wanamaker, R. A. Caldo et al., “A new resource for cereal genomics: 22K barley genechip comes of age,” Plant Physiology, vol. 134, no. 3, pp. 960–968, 2004. View at Publisher · View at Google Scholar
  28. J. Leymarie, E. Bruneaux, S. Gibot-Leclerc, and F. Corbineau, “Identification of transcripts potentially involved in barley seed germination and dormancy using cDNA-AFLP,” Journal of Experimental Botany, vol. 58, no. 3, pp. 425–437, 2007. View at Publisher · View at Google Scholar
  29. A. F. M. Ibrahim, P. E. Hedley, L. Cardle et al., “A comparative analysis of transcript abundance using SAGE and Affymetrix arrays,” Functional & Integrative Genomics, vol. 5, no. 3, pp. 163–174, 2005. View at Publisher · View at Google Scholar
  30. J. White, T. Pacey-Miller, A. Crawford et al., “Abundant transcripts of malting barley identified by serial analysis of gene expression (SAGE),” Plant Biotechnology Journal, vol. 4, no. 3, pp. 289–301, 2006. View at Publisher · View at Google Scholar
  31. A. Fischer, A. Lenhard, H. Tronecker et al., “iGentifier: indexing and large-scale profiling of unknown transcriptomes,” Nucleic Acids Research, vol. 35, no. 14, pp. 4640–4648, 2007. View at Publisher · View at Google Scholar
  32. M. Strickert, N. Sreenivasulu, B. Usadel, and U. Seiffert, “Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue,” BMC Bioinformatics, vol. 8, article 165, pp. 1–11, 2007. View at Publisher · View at Google Scholar
  33. E. Potokina, N. Sreenivasulu, L. Altschmied, W. Michalek, and A. Graner, “Differential gene expression during seed germination in barley (Hordeum vulgare L.),” Functional & Integrative Genomics, vol. 2, no. 1-2, pp. 28–39, 2002. View at Publisher · View at Google Scholar
  34. Z. W. Luo, E. Potokina, A. Druka, R. Wise, R. Waugh, and M. J. Kearsey, “SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators,” Genetics, vol. 176, no. 2, pp. 789–800, 2007. View at Publisher · View at Google Scholar
  35. A. Ueda, A. Kathiresan, J. Bennett, and T. Takabe, “Comparative transcriptome analyses of barley and rice under salt stress,” Theoretical and Applied Genetics, vol. 112, no. 7, pp. 1286–1294, 2006. View at Publisher · View at Google Scholar
  36. V. Talamé, N. Z. Ozturk, H. J. Bohnert, and R. Tuberosa, “Barley transcript profiles under dehydration shock and drought stress treatments: a comparative analysis,” Journal of Experimental Botany, vol. 58, no. 2, pp. 229–240, 2007. View at Publisher · View at Google Scholar
  37. H. Walia, C. Wilson, P. Condamine, X. Liu, A. M. Ismail, and T. J. Close, “Large-scale expression profiling and physiological characterization of jasmonic acid-mediated adaptation of barley to salinity stress,” Plant, Cell & Environment, vol. 30, no. 4, pp. 410–421, 2007. View at Publisher · View at Google Scholar
  38. R. A. Caldo, D. Nettleton, and R. P. Wise, “Interaction-dependent gene expression in Mla-specified response to barley powdery mildew,” Plant Cell, vol. 16, no. 9, pp. 2514–2528, 2004. View at Publisher · View at Google Scholar
  39. T. Gjetting, P. H. Hagedorn, P. Schweizer, H. Thordal-Christensen, T. L. W. Carver, and M. F. Lyngkjær, “Single-cell transcript profiling of barley attacked by the powdery mildew fungus,” Molecular Plant-Microbe Interactions, vol. 20, no. 3, pp. 235–246, 2007. View at Publisher · View at Google Scholar
  40. R. P. Wise, M. J. Moscou, A. J. Bogdanove, and S. A. Whitham, “Transcript profiling in host-pathogen interactions,” Annual Review of Phytopathology, vol. 45, pp. 329–369, 2007. View at Publisher · View at Google Scholar
  41. L. Shen, J. Gong, R. A. Caldo et al., “BarleyBase—an expression profiling database for plant genomics,” Nucleic Acids Research, vol. 33, pp. D614–D618, 2005. View at Publisher · View at Google Scholar
  42. U. Wobus, N. Sreenivasulu, L. Borisjuk et al., “Molecular physiology and genomics of developing barley grains,” in Recent Research Developments in Plant Molecular Biology, vol. 2, pp. 1–29, Research Signpost, Kerala, India, 2005. View at Google Scholar
  43. V. V. Radchuk, N. Sreenivasulu, R. I. Radchuk, U. Wobus, and W. Weschke, “The methylation cycle and its possible functions in barley endosperm development,” Plant Molecular Biology, vol. 59, no. 2, pp. 289–307, 2005. View at Publisher · View at Google Scholar
  44. M. B. Sørensen, “Methylation of B-hordein genes in barley endosperm is inversely correlated with gene activity and affected by the regulatory gene Lys3,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 9, pp. 4119–4123, 1992. View at Publisher · View at Google Scholar
  45. M. E. Nielsen, F. Lok, and H. B. Nielsen, “Distinct developmental defense activations in barley embryos identified by transcriptome profiling,” Plant Molecular Biology, vol. 61, no. 4-5, pp. 589–601, 2006. View at Publisher · View at Google Scholar
  46. E. Potokina, M. Caspers, M. Prasad et al., “Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.),” Molecular Breeding, vol. 14, no. 2, pp. 153–170, 2004. View at Publisher · View at Google Scholar
  47. E. Potokina, A. Druka, Z. Luo, R. Wise, R. Waugh, and M. J. Kearsey, “Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation,” The Plant Journal, vol. 53, no. 1, pp. 90–101, 2008. View at Publisher · View at Google Scholar
  48. R. Waugh, D. J. Leader, N. McCallum, and D. Caldwell, “Harvesting the potential of induced biological diversity,” Trends in Plant Science, vol. 11, no. 2, pp. 71–79, 2006. View at Publisher · View at Google Scholar
  49. D. G. Caldwell, N. McCallum, P. Shaw, G. J. Muehlbauer, D. F. Marshall, and R. Waugh, “A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.),” The Plant Journal, vol. 40, no. 1, pp. 143–150, 2004. View at Publisher · View at Google Scholar
  50. T. Koprek, D. McElroy, J. Louwerse, R. Williams-Carrier, and P. G. Lemaux, “An efficient method for dispersing Ds elements in the barley genome as a tool for determining gene function,” The Plant Journal, vol. 24, no. 2, pp. 253–263, 2000. View at Publisher · View at Google Scholar
  51. L. D. Cooper, L. Marquez-Cedillo, J. Singh et al., “Mapping Ds insertions in barley using a sequence-based approach,” Molecular Genetics and Genomics, vol. 272, no. 2, pp. 181–193, 2004. View at Publisher · View at Google Scholar
  52. J. Singh, S. Zhang, C. Chen et al., “High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals,” Plant Molecular Biology, vol. 62, no. 6, pp. 937–950, 2006. View at Publisher · View at Google Scholar
  53. T. Zhao, M. Palotta, P. Langridge et al., “Mapped Ds/T-DNA launch pads for functional genomics in barley,” The Plant Journal, vol. 47, no. 5, pp. 811–826, 2006. View at Publisher · View at Google Scholar
  54. M. A. Ayliffe, M. Pallotta, P. Langridge, and A. J. Pryor, “A barley activation tagging system,” Plant Molecular Biology, vol. 64, no. 3, pp. 329–347, 2007. View at Publisher · View at Google Scholar
  55. B. P. Forster, J. D. Franckowiak, U. Lundqvist, J. Lyon, I. Pitkethly, and W. T. B. Thomas, “The barley phytomer,” Annals of Botany, vol. 100, no. 4, pp. 725–733, 2007. View at Publisher · View at Google Scholar
  56. S. Qu, A. Desai, R. Wing, and V. Sundaresan, “A versatile transposon-based activation tag vector system for functional genomics in cereals and other monocot plants,” Plant Physiology, vol. 146, pp. 189–199, 2008. View at Publisher · View at Google Scholar
  57. P. B. Holm, O. Olsen, M. Schnorf, H. Brinch-Pedersen, and S. Knudsen, “Transformation of barley by microinjection into isolated zygote protoplasts,” Transgenic Research, vol. 9, no. 1, pp. 21–32, 2000. View at Publisher · View at Google Scholar
  58. G. Hensel, V. Valkov, J. Middlefell-Williams, and J. Kumlehn, “Efficient generation of transgenic barley: the way forward to modulate plant-microbe interactions,” Journal of Plant Physiology, vol. 165, no. 1, pp. 71–82, 2008. View at Publisher · View at Google Scholar
  59. J. Kumlehn, L. Serazetdinova, G. Hensel, D. Becker, and H. Loerz, “Genetic transformation of barley (Hordeum vulgare L.) via infection of androgenetic pollen cultures with Agrobacterium tumefaciens,” Plant Biotechnology Journal, vol. 4, no. 2, pp. 251–261, 2006. View at Publisher · View at Google Scholar
  60. D. von Wettstein, “From analysis of mutants to genetic engineering,” Annual Review of Plant Biology, vol. 58, pp. 1–19, 2007. View at Publisher · View at Google Scholar
  61. M. Kihara, Y. Okada, H. Kuroda, K. Saeki, N. Yoshigi, and K. Ito, “Improvement of β-amylase thermostability in transgenic barley seeds and transgene stability in progeny,” Molecular Breeding, vol. 6, no. 5, pp. 511–517, 2000. View at Publisher · View at Google Scholar
  62. A. Scheidig, A. Fröhlich, S. Schulze, J. R. Lloyd, and J. Kossmann, “Downregulation of a chloroplast-targeted β-amylase leads to a starch-excess phenotype in leaves,” The Plant Journal, vol. 30, no. 5, pp. 581–591, 2002. View at Publisher · View at Google Scholar
  63. J. Souppe and R. F. Beudeker, “Process for the production of alcoholic beverages using MaltSeed,” 2002, US patent no. 6361808. View at Google Scholar
  64. L. G. Jensen, O. Olsen, O. Kops, N. Wolf, K. K. Thomsen, and D. von Wettstein, “Transgenic barley expressing a protein-engineered, thermostable (1,3-1,4)-β-glucanase during germination,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 8, pp. 3487–3491, 1996. View at Publisher · View at Google Scholar
  65. H. Horvath, J. Huang, O. Wong et al., “The production of recombinant proteins in transgenic barley grains,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 4, pp. 1914–1919, 2000. View at Publisher · View at Google Scholar
  66. A. M. Nuutila, A. Ritala, R. W. Skadsen, L. Mannonen, and V. Kauppinen, “Expression of fungal thermotolerant endo-1,4-β-glucanase in transgenic barley seeds during germination,” Plant Molecular Biology, vol. 41, no. 6, pp. 777–783, 1999. View at Publisher · View at Google Scholar
  67. D. von Wettstein, G. Mikhaylenko, J. A. Froseth, and C. G. Kannangara, “Improved barley broiler feed with transgenic malt containing heat-stable (1,3-1,4)-β-glucanase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 25, pp. 13512–13517, 2000. View at Publisher · View at Google Scholar
  68. D. von Wettstein, J. Warner, and G. G. Kannangara, “Supplements of transgenic malt or grain containing (1,3-1,4)-β-glucanase increase the nutritive value of barley-based broiler diets to that of maize,” British Poultry Science, vol. 44, no. 3, pp. 438–449, 2003. View at Publisher · View at Google Scholar
  69. G. P. Xue, M. Patel, J. S. Johnson, D. J. Smyth, and C. E. Vickers, “Selectable marker-free transgenic barley producing a high level of cellulase (1,4-β-glucanase) in developing grains,” Plant Cell Reports, vol. 21, no. 11, pp. 1088–1094, 2003. View at Publisher · View at Google Scholar
  70. Y. Stahl, S. Coates, J. H. Bryce, and P. C. Morris, “Antisense downregulation of the barley limit dextrinase inhibitor modulates starch granule size distribution, starch composition and amylopectin structure,” The Plant Journal, vol. 39, no. 4, pp. 599–611, 2004. View at Publisher · View at Google Scholar
  71. M.-J. Cho, J. H. Wong, C. Marx, W. Jiang, P. G. Lemaux, and B. B. Buchanan, “Overexpression of thioredoxin h leads to enhanced activity of starch debranching enzyme (pullulanase) in barley grain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 25, pp. 14641–14646, 1999. View at Publisher · View at Google Scholar
  72. J. H. Wong, Y.-B. Kim, P.-H. Ren et al., “Transgenic barley grain overexpressing thioredoxin shows evidence that the starchy endosperm communicates with the embryo and the aleurone,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 25, pp. 16325–16330, 2002. View at Publisher · View at Google Scholar
  73. C. Sun, A.-S. Höglund, H. Olsson, E. Mangelsen, and C. Jansson, “Antisense oligodeoxynucleotide inhibition as a potent strategy in plant biology: identification of SUSIBA2 as a transcriptional activator in plant sugar signalling,” The Plant Journal, vol. 44, no. 1, pp. 128–138, 2005. View at Publisher · View at Google Scholar
  74. C. Sun, K. Ridderstråle, A.-S. Höglund, L.-G. Larsson, and C. Jansson, “Sweet delivery—sugar translocators as ports of entry for antisense oligodeoxynucleotides in plant cells,” The Plant Journal, vol. 52, no. 6, pp. 1192–1198, 2007. View at Publisher · View at Google Scholar
  75. F. Murray, R. Kalla, J. Jacobsen, and F. Gubler, “A role for HvGAMYB in anther development,” The Plant Journal, vol. 33, no. 3, pp. 481–491, 2003. View at Publisher · View at Google Scholar
  76. N. Sreenivasulu, L. Altschmied, R. Panitz et al., “Identification of genes specifically expressed in maternal and filial tissues of barley caryopses: a cDNA array analysis,” Molecular Genetics and Genomics, vol. 266, no. 5, pp. 758–767, 2001. View at Publisher · View at Google Scholar
  77. V. Radchuk, L. Borisjuk, R. Radchuk et al., “Jekyll encodes a novel protein involved in the sexual reproduction of barley,” Plant Cell, vol. 18, no. 7, pp. 1652–1666, 2006. View at Publisher · View at Google Scholar
  78. C. Künne, M. Lange, T. Funke et al., “CR-EST: a resource for crop ESTs,” Nucleic Acids Research, vol. 33, pp. D619–D621, 2005. View at Publisher · View at Google Scholar
  79. S. Weise, I. Grosse, C. Klukas et al., “Meta-All: a system for managing metabolic pathway information,” BMC Bioinformatics, vol. 7, article 465, pp. 1–9, 2006. View at Publisher · View at Google Scholar
  80. E. Grafahrend-Belau, S. Weise, D. Koschützki, U. Scholz, B. H. Junker, and F. Schreiber, “MetaCrop: a detailed database of crop plant metabolism,” Nucleic Acids Research, vol. 36, pp. D954–D958, 2008. View at Publisher · View at Google Scholar
  81. B. H. Junker, C. Klukas, and F. Schreiber, “VANTED: a system for advanced data analysis and visualization in the context of biological networks,” BMC Bioinformatics, vol. 7, article 109, pp. 1–13, 2006. View at Publisher · View at Google Scholar
  82. H. Rolletschek, W. Weschke, H. Weber, U. Wobus, and L. Borisjuk, “Energy state and its control on seed development: starch accumulation is associated with high ATP and steep oxygen gradients within barley grains,” Journal of Experimental Botany, vol. 55, no. 401, pp. 1351–1359, 2004. View at Publisher · View at Google Scholar
  83. S. Gubatz, V. J. Dercksen, C. Brüß, W. Weschke, and U. Wobus, “Analysis of barley (Hordeum vulgare) grain development using three-dimensional digital models,” The Plant Journal, vol. 52, no. 4, pp. 779–790, 2007. View at Publisher · View at Google Scholar
  84. M. Stark, B. Manz, A. Ehlers et al., “Multiparametric high-resolution imaging of barley embryos by multiphoton microscopy and magnetic resonance micro-imaging,” Microscopy Research and Technique, vol. 70, no. 5, pp. 426–432, 2007. View at Publisher · View at Google Scholar
  85. T. Neuberger, N. Sreenivasulu, M. Rokitta et al., “Quantitative imaging of oil storage in developing crop seeds,” Plant Biotechnology Journal, vol. 6, no. 1, pp. 31–45, 2008. View at Publisher · View at Google Scholar
  86. B. H. Junker, D. Koschützki, and F. Schreiber, “Kinetic modeling with the systems biology modelling environment SyBME,” Journal of Integrative Bioinformatics, vol. 3, no. 1, Article ID 0018, p. 10, 2006. View at Publisher · View at Google Scholar
  87. I. Koch, B. H. Junker, and M. Heiner, “Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber,” Bioinformatics, vol. 21, no. 7, pp. 1219–1226, 2005. View at Publisher · View at Google Scholar
  88. C. Finnie, S. Melchior, P. Roepstorff, and B. Svensson, “Proteome analysis of grain filling and seed maturation in barley,” Plant Physiology, vol. 129, no. 3, pp. 1308–1319, 2002. View at Publisher · View at Google Scholar
  89. K. Witzel, G.-K. Surabhi, G. Jyothsnakumari, C. Sudhakar, A. Matros, and H.-P. Mock, “Quantitative proteome analysis of barley seeds using ruthenium(II)-tris-(bathophenanthroline-disulphonate) staining,” Journal of Proteome Research, vol. 6, no. 4, pp. 1325–1333, 2007. View at Publisher · View at Google Scholar
  90. A. Graner, A. Jahoor, J. Schondelmaier et al., “Construction of an RFLP map of barley,” Theoretical and Applied Genetics, vol. 83, no. 2, pp. 250–256, 1991. View at Publisher · View at Google Scholar
  91. M. Heun, A. E. Kennedy, J. A. Anderson, N. L. V. Lapitan, M. E. Sorrells, and S. D. Tanksley, “Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare),” Genome, vol. 34, no. 3, pp. 437–447, 1991. View at Google Scholar
  92. A. Kleinhofs, A. Kilian, M. A. Saghai Maroof et al., “A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome,” Theoretical and Applied Genetics, vol. 86, no. 6, pp. 705–712, 1993. View at Publisher · View at Google Scholar
  93. P. M. Hayes, A. Castro, L. Marquez-Cedillo et al., “Genetic diversity for quantitatively inherited agronomic and malting quality traits,” in Diversity in Barley (Hordeum vulgare), R. von Bothmer, T. van Hintum, H. Knüpffer, and K. Sato, Eds., pp. 201–226, Elsevier Science, Amsterdam, The Netherlands, 2003. View at Google Scholar
  94. W. Friedt and F. Ordon, “Molecular markers for gene pyramiding and resistance breeding in barley,” in Genomics-Assisted Crop Improvement, Vol 2: Genomics Applications in Crops, R. Varshney and R. Tuberosa, Eds., p. 498, Springer, Berlin, Germany, 2008. View at Google Scholar
  95. T. Thiel, W. Michalek, R. K. Varshney, and A. Graner, “Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.),” Theoretical and Applied Genetics, vol. 106, no. 3, pp. 411–422, 2003. View at Publisher · View at Google Scholar
  96. R. Kota, M. Wolf, W. Michalek, and A. Graner, “Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.),” Genome, vol. 44, no. 4, pp. 523–528, 2001. View at Publisher · View at Google Scholar
  97. R. Kota, R. K. Varshney, M. Prasad, H. Zhang, N. Stein, and A. Graner, “EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome,” Functional & Integrative Genomics. In press. View at Publisher · View at Google Scholar
  98. R. Kota, S. Rudd, A. Facius et al., “Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.),” Molecular Genetics and Genomics, vol. 270, no. 1, pp. 24–33, 2003. View at Publisher · View at Google Scholar
  99. T. Thiel, R. Kota, I. Grosse, N. Stein, and A. Graner, “SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development,” Nucleic Acids Research, vol. 32, no. 1, p. e5, 2004. View at Publisher · View at Google Scholar
  100. A. Karakousis, J. P. Gustafson, K. J. Chalmers, A. R. Barr, and P. Langridge, “A consensus map of barley integrating SSR, RFLP, and AFLP markers,” Australian Journal of Agricultural Research, vol. 54, no. 11-12, pp. 1173–1185, 2003. View at Publisher · View at Google Scholar
  101. A. A. Diab, “Construction of barley consensus map showing chromosomal regions associated with economically important traits,” African Journal of Biotechnology, vol. 5, no. 3, pp. 235–248, 2006. View at Google Scholar
  102. R. K. Varshney, T. C. Marcel, L. Ramsay et al., “A high density barley microsatellite consensus map with 775 SSR loci,” Theoretical and Applied Genetics, vol. 114, no. 6, pp. 1091–1103, 2007. View at Publisher · View at Google Scholar
  103. N. Rostoks, L. Ramsay, K. MacKenzie et al., “Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varietes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 49, pp. 18656–18661, 2006. View at Publisher · View at Google Scholar
  104. P. Wenzl, J. Carling, D. Kudrna et al., “Diversity Arrays Technology (DArT) for whole-genome profiling of barley,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 26, pp. 9915–9920, 2004. View at Publisher · View at Google Scholar
  105. P. Wenzl, H. Li, J. Carling et al., “A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits,” BMC Genomics, vol. 7, article 206, pp. 1–22, 2006. View at Publisher · View at Google Scholar
  106. N. Rostoks, J. O. Borevitz, P. E. Hedley et al., “Single-feature polymorphism discovery in the barley transcriptome,” Genome Biology, vol. 6, no. 6, p. R54, 2005. View at Publisher · View at Google Scholar
  107. A. Graner and E. Bauer, “RFLP mapping of the rym4 virus resistance gene in barley,” Theoretical and Applied Genetics, vol. 86, no. 6, pp. 689–693, 1993. View at Publisher · View at Google Scholar
  108. A. Graner, S. Streng, A. Kellermann et al., “Molecular mapping and genetic fine-structure of the rym5 locus encoding resistance to different strains of the barley yellow mosaic virus complex,” Theoretical and Applied Genetics, vol. 98, no. 2, pp. 285–290, 1999. View at Publisher · View at Google Scholar
  109. N. Stein, D. Perovic, J. Kumlehn et al., “The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance in Hordeum vulgare (L.),” The Plant Journal, vol. 42, no. 6, pp. 912–922, 2005. View at Publisher · View at Google Scholar
  110. J. A. Mammadov, W. S. Brooks, C. A. Griffey, and M. A. Saghai Maroof, “Validating molecular markers for barley leaf rust resistance genes Rph5 and Rph7,” Plant Breeding, vol. 126, no. 5, pp. 458–463, 2007. View at Publisher · View at Google Scholar
  111. K. Werner, W. Friedt, and F. Ordon, “Strategies for pyramiding resistance genes against the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2),” Molecular Breeding, vol. 16, no. 1, pp. 45–55, 2005. View at Publisher · View at Google Scholar
  112. S. Salvi and R. Tuberosa, “To clone or not to clone plant QTLs: present and future challenges,” Trends in Plant Science, vol. 10, no. 6, pp. 297–304, 2005. View at Publisher · View at Google Scholar
  113. T. Sutton, U. Baumann, J. Hayes et al., “Boron-toxicity tolerance in barley arising from efflux transporter amplification,” Science, vol. 318, no. 5855, pp. 1446–1449, 2007. View at Publisher · View at Google Scholar
  114. S. J. Rae, M. Macaulay, L. Ramsay et al., “Molecular barley breeding,” Euphytica, vol. 158, no. 3, pp. 295–303, 2007. View at Publisher · View at Google Scholar
  115. W. T. B. Thomas, “Prospects for molecular breeding of barley,” Annals of Applied Biology, vol. 142, no. 1, pp. 1–12, 2003. View at Publisher · View at Google Scholar
  116. S. Doss, E. E. Schadt, T. A. Drake, and A. J. Lusis, “Cis-acting expression quantitative trait loci in mice,” Genome Research, vol. 15, no. 5, pp. 681–691, 2005. View at Publisher · View at Google Scholar
  117. D. E. Reich, M. Cargill, S. Bolk et al., “Linkage disequilibrium in the human genome,” Nature, vol. 411, no. 6834, pp. 199–204, 2001. View at Publisher · View at Google Scholar
  118. A. Rafalski and M. Morgante, “Corn and humans: recombination and linkage disequilibrium in two genomes of similar size,” Trends in Genetics, vol. 20, no. 2, pp. 103–111, 2004. View at Publisher · View at Google Scholar
  119. P. K. Gupta, S. Rustgi, and P. L. Kulwal, “Linkage disequilibrium and association studies in higher plants: present status and future prospects,” Plant Molecular Biology, vol. 57, no. 4, pp. 461–485, 2005. View at Publisher · View at Google Scholar
  120. A. T. W. Kraakman, R. E. Niks, P. M. Van den Berg, P. Stam, and F. A. Van Eeuwijk, “Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars,” Genetics, vol. 168, no. 1, pp. 435–446, 2004. View at Publisher · View at Google Scholar
  121. I. Romagosa, F. Han, S. E. Ullrich, P. M. Hayes, and D. M. Wesenberg, “Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross,” Molecular Breeding, vol. 5, no. 2, pp. 143–152, 1999. View at Publisher · View at Google Scholar
  122. J. Z. Li, X. Q. Huang, F. Heinrichs, M. W. Ganal, and M. S. Röder, “Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley,” Genome, vol. 49, no. 5, pp. 454–466, 2006. View at Publisher · View at Google Scholar
  123. L. V. Malysheva-Otto, M. W. Ganal, and M. S. Röder, “Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.),” BMC Genetics, vol. 7, article 6, pp. 1–14, 2006. View at Publisher · View at Google Scholar
  124. K. S. Caldwell, J. Russell, P. Langridge, and W. Powell, “Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare,” Genetics, vol. 172, no. 1, pp. 557–567, 2006. View at Publisher · View at Google Scholar
  125. P. L. Morrell, D. M. Toleno, K. E. Lundy, and M. T. Clegg, “Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 7, pp. 2442–2447, 2005. View at Publisher · View at Google Scholar
  126. B. J. Steffenson, P. Olivera, J. K. Roy, Y. Jin, K. P. Smith, and G. J. Muehlbauer, “A walk on the wild side: mining wild wheat and barley collections for rust resistance genes,” Australian Journal of Agricultural Research, vol. 58, no. 6, pp. 532–544, 2007. View at Publisher · View at Google Scholar
  127. S. Stracke, T. Presterl, N. Stein, D. Perovic, F. Ordon, and A. Graner, “Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley,” Genetics, vol. 175, no. 2, pp. 805–817, 2007. View at Publisher · View at Google Scholar
  128. R. C. Jansen and J.-P. Nap, “Genetical genomics: the added value from segregation,” Trends in Genetics, vol. 17, no. 7, pp. 388–391, 2001. View at Publisher · View at Google Scholar
  129. N. Sreenivasulu, R. K. Varshney, P. B. Kavi-Kishor, and W. Weschke, “Functional genomics for tolerance to abiotic stress in cereals,” in Cereal Genomics, P. K. Gupta and R. K. Varshney, Eds., pp. 483–514, Kluwer Academic Publishers, Dordrecht, The Netherlands, 2004. View at Google Scholar
  130. R. K. Varshney, A. Graner, and M. E. Sorrells, “Genomics-assisted breeding for crop improvement,” Trends in Plant Science, vol. 10, no. 12, pp. 621–630, 2005. View at Publisher · View at Google Scholar
  131. E. Potokina, M. Prasad, L. Malysheva, M. S. Röder, and A. Graner, “Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.),” Functional and Integrative Genomics, vol. 6, no. 1, pp. 25–35, 2006. View at Publisher · View at Google Scholar
  132. J. Z. Li, X. Q. Huang, F. Heinrichs, M. W. Ganal, and M. S. Röder, “Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley,” Theoretical and Applied Genetics, vol. 110, no. 2, pp. 356–363, 2005. View at Publisher · View at Google Scholar
  133. T. Wicker, E. Schlagenhauf, A. Graner, T. J. Close, B. Keller, and N. Stein, “454 sequencing put to the test using the complex genome of barley,” BMC Genomics, vol. 7, article 275, pp. 1–11, 2006. View at Publisher · View at Google Scholar
  134. G. Hammer, M. Cooper, F. Tardieu et al., “Models for navigating biological complexity in breeding improved crop plants,” Trends in Plant Science, vol. 11, no. 12, pp. 587–593, 2006. View at Publisher · View at Google Scholar
  135. X. Yin, P. C. Struik, and M. J. Kropff, “Role of crop physiology in predicting gene-to-phenotype relationships,” Trends in Plant Science, vol. 9, no. 9, pp. 426–432, 2004. View at Publisher · View at Google Scholar
  136. P. Langridge, “Molecular breeding of wheat and barley,” in The Wake of Double Helix: From the Green Revolution to the Gene Revolution, R. Tuberosa, R. L. Phillips, and M. Gale, Eds., pp. 279–286, Avenue Media, Bologna, Italy, 2005. View at Google Scholar