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New Technologies for Ultrahigh-Throughput Genotyping in Plant Taxonomy

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

Molecular genetic markers represent one of the most powerful tools for the analysis of variation between plant genomes. Molecular marker technology has developed rapidly over the last decade, with the introduction of new DNA sequencing methods and the development of high-throughput genotyping methods. Single nucleotide polymorphisms (SNPs) now dominate applications in modern plant genetic analysis. The reducing cost of DNA sequencing and increasing availability of large sequence data sets permit the mining of this data for large numbers of SNPs. These may then be used in applications such as genetic linkage analysis and trait mapping, diversity analysis, association studies, and marker-assisted selection. Here we describe automated methods for the discovery of SNP molecular markers and new technologies for high-throughput, low-cost molecular marker genotyping. Examples include SNP discovery using autoSNPdb and wheatgenome.info as well as SNP genotyping using Illumina’s GoldenGate™ and Infinium™ methods.

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References

  1. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  PubMed  Google Scholar 

  2. Edwards D, Forster JW, Chagné D, Batley J (2007) What are SNPs? In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds) Association mapping in plants. Springer, New York, pp 41–52

    Chapter  Google Scholar 

  3. Batley J, Edwards D (2007) SNP applications in plants. In: Oraguzie N, Rikkerink E, Gardiner S, De Silva H (eds) Association mapping in plants. Springer, New York, pp 95–102

    Chapter  Google Scholar 

  4. Edwards D, Forster JW, Cogan NOI, Batley J, Chagné D (2007) Single nucleotide polymorphism discovery. In: Oraguzie N, Rikkerink E, Gardiner S, De Silva H (eds) Association mapping in plants. Springer, New York, pp 53–76

    Chapter  Google Scholar 

  5. Syvanen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942

    Article  CAS  PubMed  Google Scholar 

  6. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524–535

    CAS  Google Scholar 

  7. Edwards D (2007) Bioinformatics and plant genomics for staple crops improvement. In: Kang MS, Priyadarshan PM (eds) Breeding major food staples. Blackwell, Oxford, UK, pp 93–106

    Chapter  Google Scholar 

  8. Duran C, Appleby N, Edwards D, Batley J (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinformatics 4:16–27

    Article  CAS  Google Scholar 

  9. Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Appleby N, Batley J, Basford K, Edwards D (2010) Future tools for association mapping in crop plants. Genome 53:1017–1023

    Article  CAS  PubMed  Google Scholar 

  10. Batley J, Edwards D (2009) Mining for single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) molecular genetic markers. In: Posada D (ed) Bioinformatics for DNA sequence analysis. Humana, Totowa, NJ, USA, pp 303–322

    Chapter  Google Scholar 

  11. Batley J, Edwards D (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46:333–336

    Article  CAS  PubMed  Google Scholar 

  12. Imelfort M, Duran C, Batley J, Edwards D (2009) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J 7:312–317

    Article  CAS  PubMed  Google Scholar 

  13. Berkman PJ, Lai K, Lorenc MT, Edwards D (2012) Next generation sequencing applications for wheat crop improvement. Am J Bot 99:365–371

    Article  CAS  PubMed  Google Scholar 

  14. Lee H, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D (2012) Bioinformatics tools and databases for analysis of next generation sequence data. Brief Funct Genomics 2:12–24

    Article  Google Scholar 

  15. Barker G, Batley J, O’Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19:421–422

    Article  CAS  PubMed  Google Scholar 

  16. Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker G, Spangenberg GC, Edwards D (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 33:W493–W495

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951–D953

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J (2009) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnol J 7:326–333

    Article  CAS  PubMed  Google Scholar 

  20. Lai K, Lorenc MT, Edwards D (2012) Genomic databases for crop improvement. Agronomy 2:62–73

    Article  Google Scholar 

  21. Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden MJ, Forrest KL, Fleury D, Baumann U, Zander M, Mason AS, Batley J, Edwards D (2012) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J 10:743–749

    Article  CAS  PubMed  Google Scholar 

  22. Hayward, A.; Vighnes, h. G.; Delay, G.; Samian, M. R.; Manoli, S. M.; Stiller, J.; McKenzie, M.; Edwards, D.; Batley, J. (2012) Second generation sequencing for gene discovery in the brassicaceae. Plant Biotechnol J. 10(6):750–759

    Google Scholar 

  23. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 7:1–8

    Article  Google Scholar 

  24. Arnaoudova EG, Bowens PJ, Chui RG, Dinkins RD, Hesse U, Jaromczyk JW, Martin M, Maynard P, Moore N, Schardl CL (2009) Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports. BMC Bioinformatics 10(Suppl 7):A4

    Google Scholar 

  25. Meintjes P, Duran C, Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Thierer T, Ashton B, Heled J (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649

    Article  PubMed  Google Scholar 

  26. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu FL, Yang HM, Chang LY, Huang W, Liu B, Shen Y, Tam PKH, Tsui LC, Waye MMY, Wong JTF, Zeng CQ, Zhang QR, Chee MS, Galver LM, Kruglyak S, Murray SS, Oliphant AR, Montpetit A, Hudson TJ, Chagnon F, Ferretti V, Leboeuf M, Phillips MS, Verner A, Kwok PY, Duan SH, Lind DL, Miller RD, Rice JP, Saccone NL, Taillon-Miller P, Xiao M, Nakamura Y, Sekine A, Sorimachi K, Tanaka T, Tanaka Y, Tsunoda T, Yoshino E, Bentley DR, Deloukas P, Hunt S, Powell D, Altshuler D, Gabriel SB, Qiu RZ, Ken A, Dunston GM, Kato K, Niikawa N, Knoppers BM, Foster MW, Clayton EW, Wang VO, Watkin J, Gibbs RA, Belmont JW, Sodergren E, Weinstock GM, Wilson RK, Fulton LL, Rogers J, Birren BW, Han H, Wang HG, Godbout M, Wallenburg JC, Larcheveque P, Bellemare G, Todani K, Fujita T, Tanaka S, Holden AL, Lai EH, Collins FS, Brooks LD, McEwen JE, Guyer MS, Jordan E, Peterson JL, Spiegel J, Sung LM, Zacharia LF, Kennedy K, Dunn MG, Seabrook R, Shillito M, Skene B, Stewart JG, Valle DL, Clayton EW, Jorde LB, Belmont JW, Chakravarti A, Cho MK, Duster T, Foster MW, Jasperse M, Knoppers BM, Kwok PY, Licinio J, Long JC, Marshall PA, Ossorio PN, Wang VO, Rotimi CN, Royal CDM, Spallone P, Terry SF, Lander ES, Lai EH, Nickerson DA, Abecasis GR, Altshuler D, Bentley DR, Boehnke M, Cardon LR, Daly MJ, Deloukas P, Douglas JA, Gabriel SB, Hudson RR, Hudson TJ, Kruglyak L, Kwok PY, Nakamura Y, Nussbaum RL, Royal CDM, Schaffner SF, Sherry ST, Stein LD, Tanaka T, Int HapMap C (2003) The international HapMap project. Nature 426:789–796

    Article  CAS  Google Scholar 

  27. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubalakova M, Simkova H, Batley J, Fleury D, Dolezel J, Edwards D (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9:768–775

    Article  CAS  PubMed  Google Scholar 

  28. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H, Batley J, Dolezel J, Hernandez P, Edwards D (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appli Genet 124:423–432

    Article  CAS  Google Scholar 

  29. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2012) WheatGenome.info: an integrated database and portal for wheat genome information. Plant Cell Physiol 53:1–7

    Article  Google Scholar 

  30. Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol J 10:703–708

    Article  CAS  PubMed  Google Scholar 

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Edwards, D., Zander, M., Dalton-Morgan, J., Batley, J. (2014). New Technologies for Ultrahigh-Throughput Genotyping in Plant Taxonomy. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_8

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  • DOI: https://doi.org/10.1007/978-1-62703-767-9_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-766-2

  • Online ISBN: 978-1-62703-767-9

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