Comparative Genomics in the Triticeae

  • Catherine Feuillet
  • Jérôme Salse
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 7)


The genomes of grasses are very different in terms of size, ploidy level and chromosome number. Among them, the Triticeae species (wheat, barley, rye) have some of the largest and complex genomes. Comparative mapping studies between rice, maize, sorghum, barley and wheat have pioneered the field of plant comparative genomics a decade ago. They showed that the linear order (colinearity) of genetic markers and genes is very well conserved opening the way to accelerated map-based cloning and defining rice as a model for grasses. More recently, the availability of BAC libraries and large sets of genomic sequences including the completion of the rice genome have permitted microcolinearity studies that revealed rearrangements between the grass genomes and provided some insights into mechanisms that have shaped their genome during evolution. This review summarizes a decade of comparative genomics studies in grasses with a special emphasis on the wheat and barley genomes.


Quantitative Trait Locus Rice Chromosome Whole Genome Duplication Foxtail Millet Resistance Gene Analog 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ahn, S., and Tanksley, S.D. (1993) Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. USA 90, 7980–7984.PubMedGoogle Scholar
  2. Bailey, P.C., McKibbin, R.S., Lenton, J.R., Holdsworth, M.J., Flintham, J.E. and Gale, M.D. (1999) Genetic map locations for orthologous Vp1 genes in wheat and rice. Theor. Appl. Genet. 98, 281–284.Google Scholar
  3. Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S. and Haussler, D. (2004) Ultraconserved elements in the human genome. Science 304, 1321–1325.PubMedGoogle Scholar
  4. Bennett, M.D. and Smith, J.B. (1976) Nuclear DNA amounts in angiosperms. Philos. Trans. R Soc. Lond. B Biol. Sci. 274933, 227–274.PubMedGoogle Scholar
  5. Bennetzen, J.L. and Ramakrishna, W. (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol. Biol. 48, 821–827.PubMedGoogle Scholar
  6. Bennetzen, J.L. and Ma, J. (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr. Opin. Plant Biol. 62, 128–133.PubMedGoogle Scholar
  7. Bennetzen, J.L., Ma, J. and Devos, K.M. (2005) Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95, 127–132.PubMedGoogle Scholar
  8. Bertin, I., Zhu, J.H. and Gale, M.D. (2005) SSCP-SNP in pearl millet – a new marker system for comparative genetics. Theor. Appl. Genet. 110, 1467–1472.PubMedGoogle Scholar
  9. Bossolini, E., Wicker, T., Knobel, P.A. and Keller, B. (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J. 494, 704–717.PubMedGoogle Scholar
  10. Brueggeman, R., Rostoks, N., Kudrna, D., Kilian, A., Han, F., Chen, J., Druka, A., Steffenson, B. and Kleinhofs, A. (2002) The barley stem rust-resistance gene Rpg1 is a novel disease- resistance gene with homology to receptor kinases. Proc. Natl. Acad. Sci. USA 99, 9328–9333.PubMedGoogle Scholar
  11. Brunner, S., Keller, B. and Feuillet, C. (2003) A large rearrangement involving genes and low copy DNA interrupts the microcolinearity between rice and barley at the Rph7 locus. Genetics 164, 673–683.PubMedGoogle Scholar
  12. Brunner, S., Fengler, K., Morgante, M., Tingey, S. and Rafalski, A. (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 172, 343–360.PubMedGoogle Scholar
  13. Buell, C.R., Yuan, Q., Ouyang, S., Liu, J. et al. (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 15, 1284–1291.PubMedGoogle Scholar
  14. Calabrese, P.P., Chakravarty, S. and Vision, T.J. (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19(Suppl 1), i74–i80.PubMedGoogle Scholar
  15. Caldwell, K.S., Langridge, P. and Powell, W. (2004) Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol. 136, 3177–3190.PubMedGoogle Scholar
  16. Chalhoub, B., Belcram, H. and Caboche, M. (2004) Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size. Plant Biotech. J. 2, 181–188.Google Scholar
  17. Chantret, N., Salse, J., Sabot, F., Rahman, S. et al. (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17, 1033–1045.PubMedGoogle Scholar
  18. Chen, H., Wang, S., Xing, Y., Xu, C., Hayes, P.M. and Zhang, Q. (2005) Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley. Proc. Natl. Acad. Sci. USA 100, 2544–2549.Google Scholar
  19. Chen, M., SanMiguel, P., deOliveira, A.C., Woo, S.S., Zhang, H., Wing, R.A. and Bennetzen, J.L. (1997) Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. USA 94, 3431–3435.PubMedGoogle Scholar
  20. Chen, M., SanMiguel, P. and Bennetzen, J.L. (1998) Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148, 435–443.PubMedGoogle Scholar
  21. Collins, N.C., Thordal-Christensen, H., Lipka, V. et al. (2003) SNARE-protein-mediated disease resistance at the plant cell wall. Nature 425, 973–977.PubMedGoogle Scholar
  22. Devos, K.M., Atkinson, M.D., Chinoy, C.N., Francis, H.A., Harcourt, R.L., Koebner, R.M.D., Liu, C.J., Masojc, P., Xie, D.X. and Gale, M.D. (1993a) Chromosome rearrangements in the rye genome relative to that of wheat. Theor. Appl. Genet. 85, 673–689.Google Scholar
  23. Devos, K.M., Millan, T. and Gale, M.D. (1993b) Comparative RFLP maps of the homoeologous group2 chromosomes of wheat, rye and barley. Theor. Appl. Genet. 85, 784–792.Google Scholar
  24. Devos, K.M. and Gale, M.D. (1997) Comparative genetics in the grasses. Plant Mol. Biol. 35, 3–15.PubMedGoogle Scholar
  25. Devos, K.M. and Gale, M.D. (2000) Genome relationships: the grass model in current research. Plant Cell 12, 637–646.PubMedGoogle Scholar
  26. Devos, K.M. (2005) Updating the ‘crop circle’. Curr. Opin. Plant Biol. 8, 155–162.Google Scholar
  27. Draper, J., Mur, L.J., Jenkins, G., Ghosh-Biswas, C., Bablak, P., Hasterok, R. and Routledge, A.P.M. (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127, 1539–1555.PubMedGoogle Scholar
  28. Dubcovsky, J., Luo, M.C., Zhong, G.Y., Bransteitter, R., Desai, A., Kilian, A., Kleinhofs, A. and Dvorák, J. (1996) Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L. Genetics 1432, 983–999.Google Scholar
  29. Dubcovsky, J., Ramakrishna, W., SanMiguel, P.J., Busso, C.S., Yan, L., Shiloff, B.A. and Bennetzen, J.L. (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol. 1253, 1342–1353.PubMedGoogle Scholar
  30. Dunford, R.P., Yano, M., Kurata, N., Sasaki, T., Huestis, G., Rocheford, T. and Laurie, D.A. (2002) Comparative mapping of the Barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments. Genetics 161, 825–834.PubMedGoogle Scholar
  31. Fang, Z., Polacco, M., Chen, S., Schroeder, S., Hancock, D., Sanchez, H. and Coe, E. (2003) cMap: the comparative genetic map viewer. Bioinformatics 19, 416–417.PubMedGoogle Scholar
  32. Feng, Q., Zhang, Y., Hao, P., Wang, S. et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420, 316–320.PubMedGoogle Scholar
  33. Feuillet, C. and Keller, B. (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. USA 96, 8265–8270.PubMedGoogle Scholar
  34. Feuillet, C. and Keller, B. (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. 89, 3–10.PubMedGoogle Scholar
  35. Feuillet, C., Travella, S., Stein, N., Albar, L., Nublat, A. and Keller, B. (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc. Natl. Acad. Sci. USA 100, 15253–15258.PubMedGoogle Scholar
  36. Fu, H. and Dooner, H.K. (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 9914, 9573–9578.PubMedGoogle Scholar
  37. Gaut, B.S. and Doebley, J.F. (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 9413, 6809–6814.PubMedGoogle Scholar
  38. Gaut, B.S. (2001). Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. Genome Res. 11, 55–66.PubMedGoogle Scholar
  39. Gaut, B.S. (2002) Evolutionary dynamics of grass genomes. New Phytol. 154, 15–28.Google Scholar
  40. Goff, S.A., Ricke, D., Lan, T.H., Presting, G. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92–100.PubMedGoogle Scholar
  41. Gottwald, S., Stein, N., Borner, A., Sasaki, T. and Graner, A. (2004) The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L. Mol. Genet. Genomics 271, 426–436.PubMedGoogle Scholar
  42. Griffiths, S., Dunford, R.P., Coupland, G. and Laurie, D.A. (2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol. 131, 1855–1867.PubMedGoogle Scholar
  43. Griffiths, S., Sharp, R., Foote, T.N., Bertin, I., Wanous, M., Reader, S., Colas, I. and Moore, G. (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439, 749–752.PubMedGoogle Scholar
  44. Gu, Y.Q., Coleman-Derr, D., Kong, X. and Anderson, O.D. (2004) Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes. Plant Physiol. 135, 459–470.PubMedGoogle Scholar
  45. Gu, Y.Q., Salse, J., Coleman-Derr, D., Dupin, A., Crossman, C., Lazo, G.R., Huo, N., Belcram, H., Ravel, C., Charmet, G., Charles, M., Anderson, O.D. and Chalhoub, B. (2006) Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics 1743, 1493–1504.PubMedGoogle Scholar
  46. Guyot, R., Yahiaoui, N., Feuillet, C. and Keller, B. (2004). In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Funct. Integr. Genomics 4, 47–58.Google Scholar
  47. Hampson, S., McLysaght, A., Gaut, B. and Baldi, P. (2003) LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome. Res. 13, 1–12.Google Scholar
  48. Hasterok, R., Marasek, A., Donnison, I.S., Armstead, I., Thomas, A., King, I.P., Wolny, E., Idziak, D., Draper, J. and Jenkins, G. (2006) Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173, 349–362PubMedGoogle Scholar
  49. Herrmann, R.G., Martin, R., Busch, W., Wanner, G. and Hohmann, U. (1996) Physical and topographical mapping among Triticeae chromosomes. Symp. Soc. Exp. Biol. 50, 25–30.PubMedGoogle Scholar
  50. Hohmann, U., Endo, T.R., Gill, K.S. and Gill, B.S. (1994) Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L. Mol. Gen. Genet. 2455, 644–653.Google Scholar
  51. Huang, S.X., Sirikhachornkit, A., Faris, J.D., Su, X.J., Gill, B.S., Haselkorn, R. and Gornicki, P. (2002) Phylogenetic analysis of the acetyl-CoA carboxylase and 3- phosphoglycerate kinase loci in wheat and other grasses. Plant Mol. Biol. 48, 805–820.PubMedGoogle Scholar
  52. Inada, D.C., Bashir, A., Lee, C., Thomas, B.C., Ko. C., Goff, S.A. and Freeling, M. (2003) Conserved noncoding sequences in the grasses. Genome Res. 13, 2030–2041.PubMedGoogle Scholar
  53. International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature 436, 793–800.Google Scholar
  54. Isidore, E., Scherrer, B., Chaloub, B., Feuillet, C. and Keller, B. (2005) Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res. 15, 526–536.PubMedGoogle Scholar
  55. Jaiswal, P., Ni, J., Yap, I., Ware, D. et al. (2006) Gramene: a bird’s eye view of cereal genomes. Nucl. Acids Res. 34, 717–723.Google Scholar
  56. Janda, J., Bartos, J., Safar, J., Kubalakova, M. et al. (2004) Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat. Theor. Appl. Genet. 109, 1337–1345.PubMedGoogle Scholar
  57. Janda, J., Šafář, J., Kubaláková, M., Bartoš, J. et al. (2006) Advanced resources for plant genomics: BAC library specific for the short arm of chromosome 1B. Plant J. 47, 977–986.PubMedGoogle Scholar
  58. Kaplinsky, N.J., Braun, D.M., Penterman, J., Goff, S.A. and Freeling, M. (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc. Natl. Acad. Sci. 99, 6147–6151.PubMedGoogle Scholar
  59. Kellogg, E.A. (2001) Evolutionary history of the grasses. Plant Phys. 125, 1198–1205.Google Scholar
  60. Kilian, A., Chen, J., Han, F., Steffenson, B. and Kleinhofs, A. (1997) Towards map-based cloning of the barley stem rust resistance genes rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol. Biol. 35, 187–195.PubMedGoogle Scholar
  61. Kishimoto, N., Higo, H., Abe, K., Arai, S., Saito, A. and Higo, K. (1994) Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor. Appl. Genet. 88, 722–726.Google Scholar
  62. Koller, O.L. and Zeller, F. J. (1976) Homoeologous relation ships of rye chromosomes 4R and 7R with wheat chromosomes. Genet. Res. 28, 177–188.Google Scholar
  63. Kubalakova, M., Vrana, J., Cihalikova, J., Simkova, H. and Dolezel, J. (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 104, 1362–1372.PubMedGoogle Scholar
  64. Lai, J., Li, Y., Messing, J. and Dooner, H.K. (2005) Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA 10225, 9068–9073.PubMedGoogle Scholar
  65. La Rota, M. and Sorrells, M.E. (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4, 34–46.PubMedGoogle Scholar
  66. Leister, D., Kurth, J., Laurie, D.A., Yano, M., Sasaki, T., Devos, K., Graner, A. and Schulze-Lefert, P. (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc. Natl. Acad. Sci. USA 95, 370–375.PubMedGoogle Scholar
  67. Li, W. and Gill, B.S. (2002) The colinearity of the Sh2/A1 orthologous region in rice sorghum and maize is interrupted and accompanied by genome expansion in the Triticeae. Genetics 160, 1153–1162.PubMedGoogle Scholar
  68. Lin, Y.R., Schertz, K.F. and Paterson, A.H. (1995) Comparative analysis of QTLs affecting plant height and maturity across the poaceae, in reference to an interspecific sorghum population. Genetics 141, 391–411.PubMedGoogle Scholar
  69. Lisch, D.R., Freeling, M., Langham, R.J. and Choy, M. (2001) Mutator transposase is widespread in the grasses. Plant Physiol. 1253, 1293–1303.PubMedGoogle Scholar
  70. Lisch, D. (2002) Mutator transposons. Trends Plant Sci. 711, 498–504.PubMedGoogle Scholar
  71. Liu, C.J., Atkinson, M.D., Chinoy, C.N., Devos, K.M. and Gale, M.D. (1992) Nonhomoeologous translocations between group 4, 5, and 7 chromosomes within wheat and rye. Theor. Appl. Genet. 83, 305–312.Google Scholar
  72. Lockton, S. and Gaut, B.S. (2005) Plant conserved non-coding sequences and paralogue evolution. Trends Genet. 21, 60–65.PubMedGoogle Scholar
  73. Moore, G., Devos, K.M., Wang, Z. and Gale, M.D. (1995) Cereal genome evolution: grasses, line up and form a circle. Curr. Biol. 5, 737–739.PubMedGoogle Scholar
  74. Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A. and Rafalski, A. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 379, 997–1002.PubMedGoogle Scholar
  75. Nagamura, Y., Inoue, T., Antonio, B.A. et al. (1995) Conservation of duplicated segments between rice chromosomes 11 and 12. Breed Sci. 45, 373–376.Google Scholar
  76. Naranjo, T., Roca, A., Goicoechea, P.G. and Giraldez, R. (1987) Arm homoeology of wheat and rye chromosomes. Genome 29, 873–882.Google Scholar
  77. Naranjo, T. and Fernandez-Rueda, P. (1991) Homoeology of rye chromosome arms to wheat. Theor. Appl. Genet. 82, 577–586.Google Scholar
  78. Park, Y.J., Dixit, A., Yoo, J.W. and Bennetzen, J. (2004) Further evidence of microcolinearity between barley and rice genomes at two orthologous regions. Mol. Cells 173, 492–502.PubMedGoogle Scholar
  79. Paterson, A.H., Lin, Y.R., Li, Z.K., Schertz, K.F., Doebley, J.F., Pinson, S.R.M., Liu, S.C., Stansel, J.W. and Irvine, J.E. (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269, 1714–1718.PubMedGoogle Scholar
  80. Paterson, A.H., Bowers, J.E. and Chapman, B.A. (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101, 9903–9908.PubMedGoogle Scholar
  81. Paterson, A.H., Freeling, M. and Sasaki, T. (2005) Grains of knowledge: genomics of model cereals. Genome Res. 1512, 1643–1650.PubMedGoogle Scholar
  82. Peng, J.R., Richards, D.E., Hartley, N.M., Murphy, G.P. et al. (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261.PubMedGoogle Scholar
  83. Pourkheirandish, M., Wicker, T., Stein, N., Fujimura, T. and Komatsuda, T. (2007) Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice-barley micro collinearity by a transposition. Theor. Appl. Genet. 1148, 1357–1365.PubMedGoogle Scholar
  84. Qi, L.L., Echalier, B., Chao, S., Lazo, G.R. et al. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168, 701–712.PubMedGoogle Scholar
  85. Ramakrishna, W., Dubcovsky, Y., Park, Y.J., Busso, C.S., Emberton, J., SanMiguel, P. and Bennetzen, J.L. (2002a) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162, 1389–1400.Google Scholar
  86. Ramakrishna, W., Emberton, J., Ogden, M., SanMiguel, P. and Bennetzen, J.L. (2002b) Structural analysis of the maize Rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14, 3213–3223.Google Scholar
  87. Safar, J., Bartos, J., Janda, J., Bellec, A. et al. (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J. 39, 960–968.PubMedGoogle Scholar
  88. Salse, J., Piegu, B., Cooke, R. and Delseny, M. (2002) Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project. Nucl. Acids Res. 30, 2316–2328.PubMedGoogle Scholar
  89. Salse, J., Piegu, B., Cooke, R. and Delseny, M. (2004) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J. 38, 396–409.PubMedGoogle Scholar
  90. Salse, J. and Feuillet, C. (2007) Comparative genomics of cereals. In: R. Varshney and R. Tuberosa (Eds.), Genomics-Assisted Crop Improvement (Chapter 18). Springer Verlag, Dordrecht, The Netherlands, pp. 177–205.Google Scholar
  91. Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Masood, U., Calcagno, T., Cooke, R., Delseny, M. and Feuillet, C. (2008) Identification and characterization of conserved duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20, 11–24.PubMedGoogle Scholar
  92. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K. et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420, 312–316.PubMedGoogle Scholar
  93. Scherrer, B., Isidore, E., Klein, P., Kim, J.S., Bellec, A., Chalhoub, B., Keller, B. and Feuillet, C. (2005) Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell 17, 361–374.PubMedGoogle Scholar
  94. Singh, N.K., Raghuvanshi, S., Srivastava, S.K., Gaur, A. et al. (2004) Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct. Integr. Genomics 4, 102–117.PubMedGoogle Scholar
  95. Smith, D.B. and Flavell, R.B. (1975) Characterization of the wheat genome by renaturation kinetics. Chromosoma 50, 223–242.Google Scholar
  96. Song, R. and Messing, J. (2003) Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. USA 10015, 9055–9060.PubMedGoogle Scholar
  97. Sorrells, M.E., LaRota, M., Bermudez-Kandianis, C.E., Greene, R.A. et al. (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13, 1818–1827.PubMedGoogle Scholar
  98. Sorrells, M.E. (2004) Cereal Genomics research in the post-genomic era. In: P.K. Gupta and R.K. Varshney (Eds.), Cereal Genomics. Kluwer Academic Publishers, Dordrecht, pp. 559–584.Google Scholar
  99. Stein, N., Feuillet, C., Wicker, T., Schlagenhauf, E. and Keller, B. (2000) Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc. Natl. Acad. Sci. USA 97, 13436–13441.PubMedGoogle Scholar
  100. Stein, N. (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res. 151, 21–31.PubMedGoogle Scholar
  101. Stein, N., Prasad, M., Scholz, U., Thiel, T., Zhang, H., Wolf, M., Kota, R., Varshney, R.K., Perovic, D., Grosse, I. and Graner, A. (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114(5), 823–839.PubMedGoogle Scholar
  102. Suoniemi, A., Anamthawat-Jónsson, K., Arna, T. and Schulman, A.H. (1996a) Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant Mol. Biol. 30(6), 1321–1329.Google Scholar
  103. Suoniemi, A., Narvanto, A. and Schulman, A.H. (1996b) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol. Biol. 31(2), 295–306.Google Scholar
  104. Sutton, T., Whitford, R., Baumann, U., Dong, C., Able, J.A. and Langridge, P. (2003) The Ph2 pairing homoeologous locus of wheat (Triticum aestivum): identification of candidate meiotic genes using a comparative genetics approach. Plant J. 36(4), 443–456.PubMedGoogle Scholar
  105. Sutton, T., Baumann, U., Hayes, J., Collins, N.C., Shi, B.J., Schnurbusch, T., Hay, A., Mayo, G., Pallotta, M., Tester, M. and Langridge, P. (2007) Boron-toxicity tolerance in barley arising from efflux transporter amplification. Science 318(5855), 1446–1449.PubMedGoogle Scholar
  106. Swigonová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L. and Messing, J. (2004) Close split of sorghum and maize genome progenitors. Genome Res. 14(10A), 1916–1923.PubMedGoogle Scholar
  107. The Rice Chromosome 10 Sequencing Consortium. (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566–1569.Google Scholar
  108. The Rice Chromosome 3 Sequencing Consortium. (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 15, 1284–1291.Google Scholar
  109. The Rice Full-Length cDNA Consortium. (2003) Collection, mapping, and annotation of over 28 000 cDNA clones from japonica rice. Science 301, 376–379.Google Scholar
  110. Turner, A., Beales, J., Faure, S., Dunford, R.P. and Laurie, D.A. (2005) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310, 1031–1034.PubMedGoogle Scholar
  111. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J. and Van de Peer, Y. (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12, 1792–1801.PubMedGoogle Scholar
  112. Vandepoele, K., Simillion, C. and Van de Peer, Y. (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15, 2192–2202.PubMedGoogle Scholar
  113. Van Deynze, A.E., Nelson, J.C., O’Donoughue, L.S., Ahn, S.N., Siripoonwiwat, W., Harrington, S.E., Yglesias, E.S., Braga, D.P., McCouch, S.R. and Sorrells, M.E. (1995) Comparative mapping in grasses. Oat relationships. Mol. Gen. Genet. 249(3), 349–356.PubMedGoogle Scholar
  114. Van Deynze, A.E., Nelson, J.C., Yglesias, E.S., Harrington, S.E., Braga, D.P., McCouch, S.R. and Sorrells, M.E. (1995, Oct) Comparative mapping in grasses. Wheat relationships. Mol. Gen. Genet. 25, 248(6), 744–754.Google Scholar
  115. Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Laudencia-Chingcuanco, D., Hayden, D.M., Donze, T.J., Vivian, L.A., Stamova, B. and Coleman-Derr, D. (2006) EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor. Appl. Genet. 113(2), 186–195.PubMedGoogle Scholar
  116. Wang, X., Shi, X., Hao, B., Ge, S. and Luo, J. (2005). Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946.PubMedGoogle Scholar
  117. Waugh, R., McLean, K., Flavell, A.J., Pearce, S.R., Kumar, A., Thomas, B.B. and Powell, W. (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253(6), 687–694.PubMedGoogle Scholar
  118. Wei, F., Coe, E., Nelson, W., Bharti, A.K., Engler, F., Butler, E., Kim, H., Goicoechea, J.L., Chen, M., Lee, S., Fuks, G., Sanchez-Villeda, H., Schroeder, S., Fang, Z., McMullen, M., Davis, G., Bowers, J.E., Paterson, A.H., Schaeffer, M., Gardiner, J., Cone, K., Messing, J., Soderlund, C. and Wing, R.A. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet. 3(7), e123.PubMedGoogle Scholar
  119. Wendel, J.F., Stuber, C.W., Goodman, M.M. and Beckett, J.B. (1989) Duplicated plastid and triplicated cytosolic isozymes of triosephosphate isomerase in maize (Zea mays L.). J. Hered. 3, 218–228.Google Scholar
  120. Wicker, T., Yahiaoui, N., Guyot, R., Schlagenhauf, E., Liu, Z.D., Dubcowski, J. and Keller, B. (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell 15, 1186–1197.PubMedGoogle Scholar
  121. Wicker, T., Yahiaoui, N. and Keller, B. (2007) Contrasting rates of evolution in pm3 Loci from three wheat species and rice. Genetics 177(2), 1207–1216.PubMedGoogle Scholar
  122. Yahiaoui, N., Srichumpa, P., Dudler, R. and Keller, B. (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J. 37, 528–538.PubMedGoogle Scholar
  123. Yan, L., Loukoiannov, A., Tranquilli, G., Helguera, M., Fahima, T. and Dubcovsky, J. (2003) Positional cloning of the wheat vernalization gene VRN1. Proc. Natl. Acad. Sci. USA 100, 6263–6268.PubMedGoogle Scholar
  124. Yan, L., Loukoiannov, A., Blechl, A., Tranquilli, G., Ramakrishna, W., SanMiguel, P., Bennetzen, J.L., Echenique, V. and Dubcovsky, J. (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303, 1640–1644.PubMedGoogle Scholar
  125. Yan, L., Fu, D., Li, C., Blechl, A., Tranquilli, G., Bonafede, M., Sanchez, A., Valarik, M., Yasuda, S. and Dubcovsky, J. (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc. Natl. Acad. Sci. USA 103(51), 19581–19586.PubMedGoogle Scholar
  126. Yu, J., Hu, S., Wang, J., Wong, G.K.S. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92.PubMedGoogle Scholar
  127. Yu, J., Wang, J., Lin, W., Li, S. et al. (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, 266–281.Google Scholar

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© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Genetics, Diversity and Ecophysiology of CerealsINRA-UBP UMR 1095, Domaine de CrouelleF-63100 Clermont-FerrandFrance

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