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  • Abrouk, M., Zhang, R., Murat, F., Li, A., Pont, C., Mao, L. and Salse, J. (2012) Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole genome duplication. Plant Cell, 24, 17761792.
  • Akhunov, E.D., Akhunova, A.R., Linkiewicz, A.M. et al. (2003) Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates. Proc Natl Acad Sci USA, 100, 1083610841.
  • Akhunov, E.D., Akhunova, A.R., Anderson, O.D. et al. (2010) Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics, 11, 702.
  • Allen, A.M., Barker, G.L., Berry, S.T. et al. (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol. J. 9, 10861099.
  • Allen, A.M., Barker, G.L., Wilkinson, P. et al. (2013) Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol. J. 11, 279295.
  • Bekaert, M., Edger, P.P., Pires, J.C. and Conant, G.C. (2011) Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell, 23, 17191728.
  • Berkman, P.J., Visendi, P., Lee, H.C. et al. (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnol. J. 11, 564571.
  • Brenchley, R., Spannagl, M., Pfeifer, M. et al. (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491, 705710.
  • Cavanagh, C.R., Chao, S., Wang, S. et al. (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA, 110, 80578062.
  • Chao, S., Zhang, W., Akhunov, E., Sherman, J., Ma, Y., Luo, M. and Dubcovsky, J. (2009) Analysis of gene-derived SNP marker polymorphism in wheat (Triticum aestivum L.). Mol. Breeding, 23, 2333.
  • Coulondre, C., Miller, J.H., Farabaugh, P.J. and Gilbert, W. (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature, 274, 775780.
  • Devos, K.M., Dubcovsky, J., Dvorák, J., Chinoy, C.N. and Gale, M.D. (1995) Structural evolution of wheat chromosomes 4A, 5A and 7B and its impact on recombination. Theor. Appl. Genet. 91, 282288.
  • Dibari, B., Murat, F., Chosson, A. et al. (2012) Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. BMC Genomics, 13, 221.
  • Doyle, J.J., Flagel, L.E., Paterson, A.H., Rapp, R.A., Soltis, D.E., Soltis, P.S. and Wendel, J.F. (2008) Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 42, 443461.
  • Duran, C., Edwards, D. and Batley, J. (2009) Genetic maps and the use of synteny. Methods Mol. Biol. 513, 4155.
  • Dvorak, J. and Akhunov, E.D. (2005) Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops–Triticum alliance. Genetics, 171, 323332.
  • Dvorak, J. and Zhang, H.B. (1990) Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc Natl Acad Sci USA, 87, 96409644.
  • Dvorak, J., Zhang, H.B., Kota, R.S. and Lassner, M. (1989) Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species. Genome, 32, 10031016.
  • Dvorak, J., Akhunov, E.D., Akhunov, A.R., Deal, K.R. and Luo, M.C. (2006) Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat. Mol. Biol. Evol. 23, 13861396.
  • Edger, P.P. and Pires, J.C. (2009) Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res. 17, 699717.
  • Feldman, M. (1966a) Identification of unpaired chromosomes in F1 hybrids involving Triticum aestivum and T. timopheevii. Can. J. Genet. Cytol. 8, 144151.
  • Feldman, M. (1966b) The mechanism regulating pairing in Triticum timopheevii. Wheat Inf. Serv. 21, 12.
  • Feldman, M. and Levy, A.A. (2012b) Genome evolution due to allopolyploidization in wheat. Genetics, 192, 763774.
  • Feldman, M., Lupton, F.G.H. and Miller, T.E. (1995) Wheats. In Evolution of Crop Plants, 2nd edn (Smartt, J. and Simmonds, N.W., eds). Harlow: Longman Scientific & Technical, pp. 184192.
  • Feldman, M., Levy, A.A., Fahima, T. and Korol, A. (2012a) Genomic asymmetry in allopolyploid plants: wheat as a model. J. Exp. Bot. 63, 50455059.
  • Freeling, M., Woodhouse, M.R., Subramaniam, S., Turco, G., Lisch, D. and Schnable, J.C. (2012) Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr. Opin. Plant Biol. 15, 131139.
  • Furuta, Y., Nishikawa, K. and Yamaguchi, S. (1986) Nuclear DNA content in diploid wheat and its relatives in relation to the phylogeny of tetraploid wheat. Jpn. J. Genet. 61, 97105.
  • Gill, B.S. and Chen, P.D. (1987) Role of cytoplasm specific introgression in the evolution of the polyploid wheats. Proc Natl Acad Sci USA, 84, 68006804.
  • Hutchinson, J., Miller, T.E., Jahier, J. and Shepherd, K.W. (1982) Comparison of the chromosomes of Triticum timopheevii with related wheats using the techniques of C-banding and in situ hybridization. Theor. Appl. Genet. 64, 3140.
  • International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763768.
  • International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature, 436, 793800.
  • Jia, J., Zhao, S., Kong, X. et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 496, 9195.
  • Jiang, J. and Gill, B.S. (1994) Different species-specific chromosome translocations in Triticum timopheevii and T. turgidum support the diphyletic origin of polyploid wheats. Chromosome Res. 2, 5964.
  • Kilian, B., Ozkan, H., Deusch, O., Effgen, S., Brandolini, A., Kohl, J., Martin, W. and Salamini, F. (2007) Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mol. Biol. Evol. 24, 217227.
  • Kota, R.S. and Dvorak, J. (1988) Genomic instability in wheat induced by chromosome 6b(s) of Triticum speltoides. Genetics, 120, 10851094.
  • Lai, K., Duran, C., Berkman, P.J. et al. (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol. J. 10, 743749.
  • Lerceteau-Köhler, E., Moing, A., Guérin, G., Renaud, C., Petit, A., Rothan, C. and Denoyes, B. (2012) Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control. Theor. Appl. Genet. 124, 10591077.
  • Ling, H.Q., Zhao, S., Liu, D. et al. (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature, 496, 8790.
  • Liu, Y.G. and Tsunewaki, K. (1991) Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat. Jpn. J. Genet. 66, 617633.
  • Lucas, S.J., Akpınar, B.A., Kantar, M. et al. (2013) Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A. PLoS ONE, 8, e59542.
  • Luo, M.C., Gu, Y.Q., You, F.M. et al. (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci USA, 110, 79407945.
  • Maestra, B. and Naranjo, T. (1999) Structural chromosome differentiation between Triticum timopheevii and T. turgidum and T. aestivum. Theor. Appl. Genet. 98, 744750.
  • Murat, F., Xu, J.H., Tannier, E., Abrouk, M., Guilhot, N., Pont, C., Messing, J. and Salse, J. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res. 20, 15451557.
  • Naranjo, T. (1990) Chromosome structure of durum wheat. Theor. Appl. Genet. 79, 397400.
  • Naranjo, T., Roca, A., Goicoechea, P.G. and Giráldez, R. (1987) Arm homoeology of wheat and rye chromosomes. Genome, 29, 873882.
  • Ozkan, H. and Feldman, M. (2001b) Genotypic variation in tetraploid wheat affecting homoeologous pairing in hybrids with Aegilops peregrina. Genome, 44, 10001006.
  • Ozkan, H., Levy, A.A. and Feldman, M. (2001a) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops–Triticum) group. Plant Cell, 13, 17351747.
  • Paterson, A.H., Bowers, J.E., Bruggmann, R. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551556.
  • Pont, C., Murat, F., Confolent, C., Balzergue, S. and Salse, J. (2011) RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol. 12, R119.
  • Quraishi U.M., Abrouk, M., Bolot, S. et al. (2009) Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct. Integr. Genomics, 9, 473484.
  • Quraishi, U.M., Murat, F., Abrouk, M. et al. (2011a) Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.). Funct. Integr. Genomics, 11, 7183.
  • Quraishi, U.M., Abrouk, M., Murat, F. et al. (2011b) Cross-genome map-based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution. Plant J. 65, 745756.
  • Ren, J., Sun, D., Chen, L. et al. (2013) Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int. J. Mol. Sci. 14, 70617088.
  • Roder, M.S., Korzun, V., Gill, B.S. and Ganal, M.W. (1998a) The physical mapping of microsatellite markers in wheat. Genome, 41, 278283.
  • Roder, M.S., Korzun, V., Wendehake, K., Plaschke, J., Tixier, M.H., Leroy, P. and Ganal, M.W. (1998b) A microsatellite map of wheat. Genetics, 149, 20072023.
  • Rong, J., Feltus, F.A., Waghmare, V.N. et al. (2007) Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics, 176, 25772588.
  • Saintenac, C., Jiang, D. and Akhunov, E.D. (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol. 12, R88.
  • Salina, E.A., Lim, K.Y., Badaeva, E.D., Shcherban, A.B., Adonina, I.G., Amosova, A.V., Samatadze, T.E., Vatolina, T.Y., Zoshchuk, S.A. and Leitch, A.R. (2006) Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome, 49, 10231035.
  • Salse, J. (2012) In silico archeogenomics unveils modern plant genome organization, regulation and evolution. Curr. Opin. Plant Biol. 15, 122130.
  • Salse, J., Chagué, V., Bolot, S. et al. (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics, 9, 555.
  • Schnable, P.S., Ware, D., Fulton, R.S. et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326, 11121115.
  • Schnable, J.C., Freeling, M. and Lyons, E. (2012a) Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol. Evol. 4, 265277.
  • Schnable, J.C., Wang, X., Pires, J.C. and Freeling, M. (2012b) Escape from preferential retention following repeated whole genome duplications in plants. Front Plant Sci. 3, 94.
  • Terachi, T., Ogihara, Y. and Tsunewaki, K. (1990) The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops. 7. Restriction endonuclease analysis of mitochondrial DNA from polyploid wheats and their ancestral species. Theor. Appl. Genet. 80, 366373.
  • Thomas, B.C., Pedersen, B. and Freeling, M. (2006) Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res. 16, 934946.
  • Thuillet, A.C., Bataillon, T., Poirier, S., Santoni, S. and David, J.L. (2005) Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics, 169, 15891599.
  • Trebbi, D., Maccaferri, M., de Heer, P., Sørensen, A., Giuliani, S., Salvi, S., Sanguineti, M.C., Massi, A., van der Vossen, E.A. and Tuberosa, R. (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor. Appl. Genet. 123, 555569.
  • Trick, M., Adamski, N.M., Mugford, S.G., Jiang, C.C., Febrer, M. and Uauy, C. (2012) Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol. 12, 14.
  • 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, 937946.
  • Wang, J., Luo, M.C., Chen, Z., You, F.M., Wei, Y., Zheng, Y. and Dvorak, J. (2013) Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New Phytol. 198, 925937.
  • Wicker, T., Mayer, K.F., Gundlach, H. et al. (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell, 23, 17061718.
  • Winfield, M.O., Wilkinson, P.A., Allen, A.M. et al. (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol. J. 10, 733742.
  • Woodhouse, M.R., Schnable, J.C., Pedersen, B.S., Lyons, E., Lisch, D., Subramaniam, S. and Freeling, M. (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol. 8, e1000409.
  • You, F.M., Huo, N., Deal, K.R., Gu, Y.Q., Luo, M.C., McGuire, P.E., Dvorak, J. and Anderson, O.D. (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics, 12, 59.
  • Zhang, H., Bian, Y., Gou, X. et al. (2013) Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proc Natl Acad Sci USA, 110, 34473452.
  • Zohary, D. and Feldman, M. (1962) Hybridization between amphidiploids and the evolution of polyploids in the wheat (Aegilops–Triticum) group. Evolution, 16, 4461.