cDNA Libraries pp 225-246 | Cite as

SNP Discovery by Transcriptome Pyrosequencing

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 729)

Abstract

Single nucleotide polymorphisms (SNPs) are single base differences between haplotypes. SNPs are abundant in many species and valuable as markers for genetic map construction, modern molecular breeding programs, and quantitative genetic studies. SNPs are readily mined from genomic DNA or cDNA sequence obtained from individuals having two or more distinct genotypes. While automated Sanger sequencing has become less expensive over time, it is still costly to acquire deep Sanger sequence from several genotypes. “Next-generation” DNA sequencing technologies that utilize new chemistries and massively parallel approaches have enabled DNA sequences to be acquired at extremely high depths of coverage faster and for less cost than traditional sequencing. One such method is represented by the Roche/454 Life Sciences GS-FLX Titanium Series, which currently uses pyrosequencing to produce up to 400–600 million bases of DNA sequence/run (>1 million reads, ∼400 bp/read). This chapter discusses the use of high-throughput pyrosequencing for SNP discovery by focusing on 454 sequencing of maize cDNA, the development of a computational pipeline for polymorphism detection, and the subsequent identification of over 7,000 putative SNPs between Mo17 and B73 maize. In addition, alternative alignment and polymorphism detection strategies that implement Illumina short reads, data processing and visualization tools, and reduced representation techniques that reduce the sequencing of repeat DNA, thus enabling efficient analysis of genome sequence, are discussed.

Key words

Next-generation sequencing Pyrosequencing SNP Whole-genome SNP discovery Computational biology Maize 

Notes

Acknowledgments

We thank Sanzhen Liu (Iowa State University), Yi Jia (Iowa State University), and Cheng-Ting Eddy Yeh (Iowa State University) for comments on the manuscript; Drs. Haiyan Wu (Iowa State University and China Agriculture University), Ananth Kalyanaraman (Washington State University), Wei Wu (Iowa State University), and An-Ping Hsia (Iowa State University) for sharing Brachypodium 454 EST data prior to publication; Drs. Richard Buggs (University of Florida), Doug Soltis (University of Florida), and Pam Soltis (University of Florida) for sharing Tragopogon data prior to publication; Dr. Nathan Springer (University of Minnesota) and Dr. Jeff Jeddeloh (Roche NimbleGen Inc.) for sharing maize sequence capture data prior to publication; Dr. Scott Emrich (University of Notre Dame) for stimulating discussions; and Marianne Smith (Iowa State University) and Lisa Coffey (Iowa State University) for technical assistance. This project was supported by competitive grants from the National Science Foundation Plant Genome Program to P.S.S. (DBI-0321711, DBI-0321595, and DBI-0919254) and W.B.B. (DBI-0501758 and DBI-0919254), by the National Research Initiative (NRI) Plant Genome Program of the USDA Cooperative State Research, Education and Extension Service (CSREES) to W.B.B., and by Hatch Act and State of Iowa funds to P.S.S.

References

  1. 1.
    Gut, I. G. (2001) Automation in genotyping of single nucleotide polymorphisms. Hum. Mutat. 17, 475–492.PubMedCrossRefGoogle Scholar
  2. 2.
    Kwok, P. Y. (2001) Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2, 235–258.PubMedCrossRefGoogle Scholar
  3. 3.
    Leushner, J. and Chiu, N. H. (2000) Automated mass spectrometry: a revolutionary technology for clinical diagnostics. Mol. Diagn. 5, 341–348.PubMedGoogle Scholar
  4. 4.
    Consortium, T. I. H. (2003) The International HapMap Project. Nature 426, 789–796.CrossRefGoogle Scholar
  5. 5.
    Consortium, T. I. H. (2005) A haplotype map of the human genome. Nature 437, 1299–1320.CrossRefGoogle Scholar
  6. 6.
    Bray, N. J., Buckland, P. R., Owen, M. J., and O’Donovan, M. C. (2003) Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113, 149–153.PubMedGoogle Scholar
  7. 7.
    Cowles, C. R., Hirschhorn, J. N., Altshuler, D., and Lander, E. S. (2002) Detection of regulatory variation in mouse genes. Nat. Genet. 32, 432–437.PubMedCrossRefGoogle Scholar
  8. 8.
    Guo, M., Rupe, M. A., Zinselmeier, C., Habben, J., Bowen, B. A., and Smith, O. S. (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16, 1707–1716.PubMedCrossRefGoogle Scholar
  9. 9.
    Pastinen, T., Sladek, R., Gurd, S., Sammak, A., Ge, B., Lepage, P., Lavergne, K., Villeneuve, A., Gaudin, T., Brandstrom, H., Beck, A., Verner, A., Kingsley, J., Harmsen, E., Labuda, D., Morgan, K., Vohl, M. C., Naumova, A. K., Sinnett, D., and Hudson, T. J. (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol. Genomics 16, 184–193.PubMedGoogle Scholar
  10. 10.
    Stupar, R. M. and Springer, N. M. (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173, 2199–2210.PubMedCrossRefGoogle Scholar
  11. 11.
    Sachidanandam, R., Weissman, D., Schmidt, S. C., et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.PubMedCrossRefGoogle Scholar
  12. 12.
    Wiltshire, T., Pletcher, M. T., Batalov, S., Barnes, S. W., Tarantino, L. M., Cooke, M. P., Wu, H., Smylie, K., Santrosyan, A., Copeland, N. G., Jenkins, N. A., Kalush, F., Mural, R. J., Glynne, R. J., Kay, S. A., Adams, M. D., and Fletcher, C. F. (2003) Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc. Natl Acad. Sci. USA 100, 3380–3385.PubMedCrossRefGoogle Scholar
  13. 13.
    Feltus, F. A., Wan, J., Schulze, S. R., Estill, J. C., Jiang, N., and Paterson, A. H. (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14, 1812–1819.PubMedCrossRefGoogle Scholar
  14. 14.
    Jander, G., Norris, S. R., Rounsley, S. D., Bush, D. F., Levin, I. M., and Last, R. L. (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129, 440–450.PubMedCrossRefGoogle Scholar
  15. 15.
    Yamasaki, M., Tenaillon, M. I., Bi, I. V., Schroeder, S. G., Sanchez-Villeda, H., Doebley, J. F., Gaut, B. S., and McMullen, M. D. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17, 2859–2872.PubMedCrossRefGoogle Scholar
  16. 16.
    Marth, G. T., Korf, I., Yandell, M. D., Yeh, R. T., Gu, Z., Zakeri, H., Stitziel, N. O., Hillier, L., Kwok, P. Y., and Gish, W. R. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452–456.PubMedCrossRefGoogle Scholar
  17. 17.
    Dantec, L. L., Chagne, D., Pot, D., Cantin, O., Garnier-Gere, P., Bedon, F., Frigerio, J. M., Chaumeil, P., Leger, P., Garcia, V., Laigret, F., De Daruvar, A., and Plomion, C. (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol. Biol. 54, 461–470.PubMedCrossRefGoogle Scholar
  18. 18.
    Kota, R., Rudd, S., Facius, A., Kolesov, G., Thiel, T., Zhang, H., Stein, N., Mayer, K., and Graner, A. (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol. Genet. Genomics 270, 24–33.PubMedCrossRefGoogle Scholar
  19. 19.
    Kota, R., Varshney, R. K., Thiel, T., Dehmer, K. J., and Graner, A. (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135, 145–151.PubMedCrossRefGoogle Scholar
  20. 20.
    Lopez, C., Piegu, B., Cooke, R., Delseny, M., Tohme, J., and Verdier, V. (2005) Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor. Appl. Genet. 110, 425–431.PubMedCrossRefGoogle Scholar
  21. 21.
    Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., and Schnable, P. S. (2007) SNP discovery via 454 transcriptome sequencing. Plant J. 51, 910–918.PubMedCrossRefGoogle Scholar
  22. 22.
    Batley, J., Barker, G., O’Sullivan, H., Edwards, K. J., and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol. 132, 84–91.PubMedCrossRefGoogle Scholar
  23. 23.
    Holt, R. A. and Jones, S. J. (2008) The new paradigm of flow cell sequencing. Genome Res. 18, 839–846.PubMedCrossRefGoogle Scholar
  24. 24.
    Margulies, M., Egholm, M., Altman, W. E., et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.PubMedGoogle Scholar
  25. 25.
    Bentley, D. R. (2006) Whole-genome ­re-sequencing, Curr. Opin. Genet. Dev. 16, 545–552.PubMedCrossRefGoogle Scholar
  26. 26.
    Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res. 9, 868–877.PubMedCrossRefGoogle Scholar
  27. 27.
    Sundquist, A., Ronaghi, M., Tang, H., Pevzner, P., and Batzoglou, S. (2007) Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One 2, e484.PubMedCrossRefGoogle Scholar
  28. 28.
    Quinlan, A. R., Stewart, D. A., Stromberg, M. P., and Marth, G. T. (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat. Methods 5, 179–181.PubMedCrossRefGoogle Scholar
  29. 29.
    Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., and Welch, D. M. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8, R143.PubMedCrossRefGoogle Scholar
  30. 30.
    Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.PubMedGoogle Scholar
  31. 31.
    Goldberg, S. M., Johnson, J., Busam, D., et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl Acad. Sci. USA 103, 11240–11245.PubMedCrossRefGoogle Scholar
  32. 32.
    Hiller, N. L., Janto, B., Hogg, J. S., Boissy, R., Yu, S., Powell, E., Keefe, R., Ehrlich, N. E., Shen, K., Hayes, J., Barbadora, K., Klimke, W., Dernovoy, D., Tatusova, T., Parkhill, J., Bentley, S. D., Post, J. C., Ehrlich, G. D., and Hu, F. Z. (2007) Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J. Bacteriol. 189, 8186–8195.PubMedCrossRefGoogle Scholar
  33. 33.
    Hofreuter, D., Tsai, J., Watson, R. O., Novik, V., Altman, B., Benitez, M., Clark, C., Perbost, C., Jarvie, T., Du, L., and Galan, J. E. (2006) Unique features of a highly pathogenic Campylobacter jejuni strain. Infect. Immun. 74, 4694–4707.PubMedCrossRefGoogle Scholar
  34. 34.
    Pearson, B. M., Gaskin, D. J., Segers, R. P., Wells, J. M., Nuijten, P. J., and van Vliet, A. H. (2007) The complete genome sequence of Campylobacter jejuni strain 81116 (NCTC11828). J. Bacteriol. 189, 8402–8403.PubMedCrossRefGoogle Scholar
  35. 35.
    Smith, M. G., Gianoulis, T. A., Pukatzki, S., Mekalanos, J. J., Ornston, L. N., Gerstein, M., and Snyder, M. (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 21, 601–614.PubMedCrossRefGoogle Scholar
  36. 36.
    Warren, R. L., Sutton, G. G., Jones, S. J., and Holt, R. A. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23, 500–501.PubMedCrossRefGoogle Scholar
  37. 37.
    Jeck, W. R., Reinhardt, J. A., Baltrus, D. A., Hickenbotham, M. T., Magrini, V., Mardis, E. R., Dangl, J. L., and Jones, C. D. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23, 2942–2944.PubMedCrossRefGoogle Scholar
  38. 38.
    Dohm, J. C., Lottaz, C., Borodina, T., and Himmelbauer, H. (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17, 1697–1706.PubMedCrossRefGoogle Scholar
  39. 39.
    Henderson, I. R., Zhang, X., Lu, C., Johnson, L., Meyers, B. C., Green, P. J., and Jacobsen, S. E. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 38, 721–725.PubMedCrossRefGoogle Scholar
  40. 40.
    Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I. A., Belmonte, M. K., Lander, E. S., Nusbaum, C., and Jaffe, D. B. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810–820.PubMedCrossRefGoogle Scholar
  41. 41.
    Zerbino, D. R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829.PubMedCrossRefGoogle Scholar
  42. 42.
    Andries, K., Verhasselt, P., Guillemont, J., Gohlmann, H. W., Neefs, J. M., Winkler, H., Van Gestel, J., Timmerman, P., Zhu, M., Lee, E., Williams, P., de Chaffoy, D., Huitric, E., Hoffner, S., Cambau, E., Truffot-Pernot, C., Lounis, N., and Jarlier, V. (2005) A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307, 223–227.PubMedCrossRefGoogle Scholar
  43. 43.
    Eveland, A. L., McCarty, D. R., and Koch, K. E. (2008) Transcript profiling by 3′-untranslated region sequencing resolves expression of gene families. Plant Physiol. 146, 32–44.PubMedCrossRefGoogle Scholar
  44. 44.
    Johnson, D. S., Mortazavi, A., Myers, R. M., and Wold, B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502.PubMedCrossRefGoogle Scholar
  45. 45.
    Novaes, E., Drost, D. R., Farmerie, W. G., Pappas, G. J., Jr., Grattapaglia, D., Sederoff, R. R., and Kirst, M. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9, 312.PubMedCrossRefGoogle Scholar
  46. 46.
    Van Tassell, C. P., Smith, T. P., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C. T., Haudenschild, C. D., Moore, S. S., Warren, W. C., and Sonstegard, T. S. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5, 247–252.PubMedCrossRefGoogle Scholar
  47. 47.
    Buggs, R. J. A., Chamala, S., Wu, W., Gao, L., May, G. D., Schnable, P. S., Soltis, D. E., Soltis, P. S., and Barbazuk, W. B. (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol. Ecol. 19(S1), 132–146.PubMedCrossRefGoogle Scholar
  48. 48.
    Emrich, S. J., Barbazuk, W. B., Li, L., and Schnable, P. S. (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17, 69–73.PubMedCrossRefGoogle Scholar
  49. 49.
    Hillier, L. W., Marth, G. T., Quinlan, A. R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J. I., Hickenbotham, M., Huang, W., Magrini, V. J., Richt, R. J., Sander, S. N., Stewart, D. A., Stromberg, M., Tsung, E. F., Wylie, T., Schedl, T., Wilson, R. K., and Mardis, E. R. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5, 183–188.PubMedCrossRefGoogle Scholar
  50. 50.
    Emrich, S. J., Aluru, S., Fu, Y., Wen, T. J., Narayanan, M., Guo, L., Ashlock, D. A., and Schnable, P. S. (2004) A strategy for assembling the maize (Zea mays L.) genome. Bioinformatics 20, 140–147.PubMedCrossRefGoogle Scholar
  51. 51.
    Pertea, G., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y., White, J., Cheung, F., Parvizi, B., Tsai, J., and Quackenbush, J. (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651–652.PubMedCrossRefGoogle Scholar
  52. 52.
    Huang, W. and Marth, G. (2008) EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 18, 1538–1543PubMedCrossRefGoogle Scholar
  53. 53.
    Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8, 195–202.PubMedGoogle Scholar
  54. 54.
    Manaster, C., Zheng, W., Teuber, M., Wachter, S., Doring, F., Schreiber, S., and Hampe, J. (2005) InSNP: a tool for automated detection and visualization of SNPs and InDels. Hum. Mutat. 26, 11–19.PubMedCrossRefGoogle Scholar
  55. 55.
    Nickerson, D. A., Tobe, V. O., and Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745–2751.PubMedCrossRefGoogle Scholar
  56. 56.
    Wang, J. and Huang, X. (2005) A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. BMC Bioinform. 6, 220.CrossRefGoogle Scholar
  57. 57.
    Weckx, S., Del-Favero, J., Rademakers, R., Claes, L., Cruts, M., De Jonghe, P., Van Broeckhoven, C., and De Rijk, P. (2005) novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 15, 436–442.PubMedCrossRefGoogle Scholar
  58. 58.
    Zhang, J., Wheeler, D. A., Yakub, I., Wei, S., Sood, R., Rowe, W., Liu, P. P., Gibbs, R. A., and Buetow, K. H. (2005) SNP detector: A software tool for sensitive and accurate SNP detection. PLoS Comput. Biol. 1, e53.PubMedCrossRefGoogle Scholar
  59. 59.
    Schnable, P. S., Ware, D., Fulton, R. S., et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112–1115.PubMedCrossRefGoogle Scholar
  60. 60.
    Fu, Y., Emrich, S. J., Guo, L., Wen, T. J., Ashlock, D. A., Aluru, S., and Schnable, P. S. (2005) Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl Acad. Sci. USA 102, 12282–12287.PubMedCrossRefGoogle Scholar
  61. 61.
    Whitelaw, C. A., Barbazuk, W. B., Pertea, G., Chan, A. P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J. L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M. A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy, R., Fraser, C. M., and Quackenbush, J. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302, 2118–2120.PubMedCrossRefGoogle Scholar
  62. 62.
    Emrich, S. J., Li, L., Wen, T. J., Yandeau-Nelson, M. D., Fu, Y., Guo, L., Chou, H. H., Aluru, S., Ashlock, D. A., and Schnable, P. S. (2007) Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution. Genetics 175, 429–439.PubMedCrossRefGoogle Scholar
  63. 63.
    Liu, S., Chen, H. D., Makarevitch, I., Shirmer, R., Emrich, S. J., Dietrich, C. R., Barbazuk, W. B., Springer, N. M., and Schnable, P. S. (2009) High-throughput genetic mapping of mutants via quantitative SNP-typing. Genetics 184, 19–26.PubMedCrossRefGoogle Scholar
  64. 64.
    The International Brachypodium Initiative. (2010) Genome sequence and analysis of the model grass Brachypodium distachyon. Nature 463, 763–768.CrossRefGoogle Scholar
  65. 65.
    Kalyanaraman, A., Aluru, S., Kothari, S., and Brendel, V. (2003) Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Res. 31, 2963–2974.PubMedCrossRefGoogle Scholar
  66. 66.
    Kalyanaraman, A., Aluru, S., Kothari, S., and Brendel, V. (2003) Space and time efficient parallel algorithms and software for EST ­clustering. IEEE Transactions on Parallel and Distributed Systems (TPDS) 14, 1209–1221.CrossRefGoogle Scholar
  67. 67.
    Bennetzen, J. L., Schrick, K., Springer, P. S., Brown, W. E., and SanMiguel, P. (1994) Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565–576.PubMedCrossRefGoogle Scholar
  68. 68.
    Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., Carrington, J. C., Doerge, R. W., Colot, V., and Martienssen, R. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476.PubMedCrossRefGoogle Scholar
  69. 69.
    Rabinowicz, P. D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L. D., Stein, L., McCombie, W. R., and Martienssen, R. A. (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat. Genet. 23, 305–308.PubMedCrossRefGoogle Scholar
  70. 70.
    Bedell, J., Budiman, M., Nunberg, A., Citek, R., Robbins, D., et al., (2005) Sorghum genome sequencing by methylation filtration. PloS Biol. 3, e13.PubMedCrossRefGoogle Scholar
  71. 71.
    Altshuler, D., Pollara, V. J., Cowles, C. R., Van Etten, W. J., Baldwin, J., Linton, L., and Lander, E. S. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516.PubMedCrossRefGoogle Scholar
  72. 72.
    Burr, B., Burr, F. A., Thompson, K. H., Albertson, M. C., and Stuber, C. W. (1988) Gene mapping with recombinant inbreds in maize. Genetics 118, 519–526.PubMedGoogle Scholar
  73. 73.
    Emberton, J., Ma, J., Yuan, Y., SanMiguel, P., and Bennetzen, J. L. (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 10, 1441–1446.CrossRefGoogle Scholar
  74. 74.
    Britten, R. J., Graham, D. E., and Neufeld, B. R. (1974) Analysis of repeating DNA sequences by reassociation. Methods Enzymol. 29, 363–418.PubMedCrossRefGoogle Scholar
  75. 75.
    Peterson, D. G., Wessler, S. R., and Paterson, A. H. (2002) Efficient capture of unique sequences from eukaryotic genomes. Trends Genet. 18, 547–550.PubMedCrossRefGoogle Scholar
  76. 76.
    Yuan, Y., SanMiguel, P. J., and Bennetzen, J. L. (2003) High-Cot sequence analysis of the maize genome. Plant J. 34, 249–255.PubMedCrossRefGoogle Scholar
  77. 77.
    Barbazuk, W. B., Bedell, J. A., and Rabinowicz, P. D. (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27, 839–848.PubMedCrossRefGoogle Scholar
  78. 78.
    Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., 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, 903–905.PubMedCrossRefGoogle Scholar
  79. 79.
    D’Ascenzo, M., Meacham, C., Kitzman, J., Middle, C., Knight, J., Winer, R., Kukricar, M., Richmond, T., Albert, T. J., Czechanski, A., Donahue, L. R., Affourtit, J., Jeddeloh, J. A., and Reinholdt, L. (2009) Mutation discovery in the mouse using genetically guided array capture and resequencing. Mamm. Genome 20, 424–436.PubMedCrossRefGoogle Scholar
  80. 80.
    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, 1522–1527.PubMedCrossRefGoogle Scholar
  81. 81.
    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, 907–909.PubMedCrossRefGoogle Scholar
  82. 82.
    Fu, Y., Springer, N. M., Gerhardt, D. J., Ying, K., Yeh, C-T., Wu, W., Swanson-Wagner, R., D’Ascenzo, D., 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, 898–909.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Biology and the Genetics InstituteUniversity of FloridaGainesvilleUSA
  2. 2.Department of Agronomy, Center for Plant GenomicsIowa State UniversityAmesUSA

Personalised recommendations