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  • Aitken, K.S., Jackson, P.A. and McIntyre, C.L. (2005) A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theor. Appl. Genet. 110, 789801.
  • Albert, T.J., Molla, M.N., Muzny, D.M., Nazareth, L., Wheeler, D., Song, X.Z., Richmond, T.A., Middle, C.M., Rodesch, M.J., Packard, C.J., Weinstock, G.M. and Gibbs, R.A. (2007) Direct selection of human genomic loci by microarray hybridization. Nat. Methods, 4, 903905.
  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403410.
  • Bashiardes, S., Veile, R., Helms, C., Mardis, E.R., Bowcock, A.M. and Lovett, M. (2005) Direct genomic selection. Nat. Methods, 2, 6369.
  • Bell, G.I., Pictet, R.L., Rutter, W.J., Cordell, B., Tischer, E. and Goodman, H.M. (1980) Sequence of the human insulin gene. Nature, 284, 2632.
  • Bundock, P.C., Eliott, F.G., Ablett, G., Benson, A.D., Casu, R.E., Aitken, K.S. and Henry, R.J. (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J. 7, 347354.
  • Dahl, F., Gullberg, M., Stenberg, J., Landegren, U. and Nilsson, M. (2005) Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments. Nucleic Acids Res. 33 (8), e71.
  • Dahl, F., Stenberg, J., Fredriksson, S., Welch, K., Zhang, M., Nilsson, M., Bicknell, D., Bodmer, W.F., Davis, R.W. and Ji, H. (2007) Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc. Natl Acad. Sci. USA, 104, 93879392.
  • Fu, Y., Springer, N.M., Gerhardt, D.J., Ying, K., Yeh, C.T., Wu, W., Swanson-Wagner, R., D’Ascenzo, M., Millard, T., Freeberg, L., Aoyama, N., Kitzman, J., Burgess, D., Richmond, T., Albert, T.J., Barbazuk, W.B., Jeddeloh, J.A. and Schnable, P.S. (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J. 62, 898909.
  • Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D.B., Lander, E.S. and Nusbaum, C. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182189.
  • Grunstein, M. and Hogness, D.S. (1975) Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc. Natl Acad. Sci. USA, 72, 39613965.
  • Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E.A., Karlin- Neumann, G.A., Fakhrai-Rad, H., Ronaghi, M., Willis, T.D., Landegren, U. and Davis, R.W. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673678.
  • Hardenbol, P., Yu, F.L., Belmont, J., MacKenzie, J., Bruckner, C., Brundage, T., Boudreau, A., Chow, S., Eberle, J., Erbilgin, A., Falkowski, M., Fitzgerald, R., Ghose, S., Iartchouk, O., Jain, M., Karlin-Neumann, G., Lu, X.H., Miao, X., Moore, B., Moorhead, M., Namsaraev, E., Pasternak, S., Prakash, E., Tran, K., Wang, Z.Y., Jones, H.B., Davis, R.W., Willis, T.D. and Gibbs, R.A. (2005) Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15, 269275.
  • Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M.N., Smith, S.W., Middle, C.M., Rodesch, M.J., Albert, T.J., Hannon, G.J. and McCombie, W.R. (2007) Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 15221527.
  • Kharabian-Masouleh, A., Waters, D.L.E., Reinke, R.F. and Henry, R.J. (2011) Discovery of polymorphisms in starch related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotechnol. J. 9, 10741085.
  • Lovett, M., Kere, J. and Hinton, L.M. (1991) Direct selection—a method for the isolation of cDNAs encoded by large genomic regions. Proc. Natl Acad. Sci. USA, 88, 96289632.
  • Malory, S., Shapter, F.M., Elphinstone, M.S., Chivers, I.H. and Henry, R.J. (2011) Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes. Plant Biotechnol. J. 9, 11311140.
  • Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., Kumar, A., Howard, E., Shendure, J. and Turner, D.J. (2010) Target-enrichment strategies for next generation sequencing. Nat. Methods, 7, 111118.
  • Morgan, J.G., Dolganov, G.M., Robbins, S.E., Hinton, L.M. and Lovett, M. (1992) The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin-4 and interleukin-5 genes. Nucleic Acids Res. 20, 51735179.
  • Mullis, K.B. and Faloona, F.A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain-reaction. Methods Enzymol. 155, 335350.
  • Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E.E., Bamshad, M., Nickerson, D.A. and Shendure, J. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272276.
  • Ng, S.B., Bigham, A.W., Buckingham, K.J., Hannibal, M.C., McMillin, M.J., Gildersleeve, H.I., Beck, A.E., Tabor, H.K., Cooper, G.M., Mefford, H.C., Lee, C., Turner, E.H., Smith, J.D., Rieder, M.J., Yoshiura, K., Matsumoto, N., Ohta, T., Niikawa, N., Nickerson, D.A., Bamshad, M.J. and Shendure, J. (2010a) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790793.
  • Ng, S.B., Buckingham, K.J., Lee, C., Bigham, A.W., Tabor, H.K., Dent, K.M., Huff, C.D., Shannon, P.T., Jabs, E.W., Nickerson, D.A., Shendure, J. and Bamshad, M.J. (2010b) Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42, 3035.
  • Okou, D.T., Steinberg, K.M., Middle, C., Cutler, D.J., Albert, T.J. and Zwick, M.E. (2007) Microarray-based genomic selection for high-throughput resequencing. Nat. Methods, 4, 907909.
  • Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H., Wang, X., Wicker, T., Bharti, A.K., Chapman, J., Feltus, F.A., Gowik, U., Grigoriev, I.V., Lyons, E., Maher, C.A., Martis, M., Narechania, A., Otillar, R.P., Penning, B.W., Salamov, A.A., Wang, Y., Zhang, L., Carpita, N.C., Freeling, M., Gingle, A.R., Hash, C.T., Keller, B., Klein, P., Kresovich, S., McCann, M.C., Ming, R., Peterson, D.G., Mehboob-Ur-Rahman, Ware, D., Westhoff, P., Mayer, K.F., Messing, J. and Rokhsar, D.S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551556.
  • Souza, G.M., Berges, H., Bocs, S., Casu, R., D’Hont, A., Ferreira, J.E., Henry, R., Ming Potier, R.B., Van Sluys, M.A., Vincentz, M. and Paterson, A.H. (2011) The sugarcane genome challenges: strategies for sequencing a highly complex genome. Trop. Plant Biol. 4, 145156.
  • Tewhey, R., Nakano, M., Wang, X.Y., Pabon-Pena, C., Novak, B., Giuffre, A., Lin, E., Happe, S., Roberts, D.N., LeProust, E.M., Topol, E.J., Harismendy, O. and Frazer, K.A. (2009a) Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 10, R116.
  • Tewhey, R., Warner, J.B., Nakano, M., Libby, B., Medkova, M., David, P.H., Kotsopoulos, S.K., Samuels, M.L., Hutchison, J.B., Larson, J.W., Topol, E.J., Weiner, M.P., Harismendy, O., Olson, J., Link, D.R. and Frazer, K.A. (2009b) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol. 27, 10251031.
  • Turner, E.H., Lee, C.L., Ng, S.B., Nickerson, D.A. and Shendure, J. (2009) Massively parallel exon capture and library-free resequencing across 16 genomes. Nat. Methods, 6, 315316.
  • Winfield, M.O., Lu, C.G., Wilson, I.D., Coghill, J.A. and Edwards, K.J. (2010) Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol. J. 8, 749771.