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Advances in Plant Genotyping: Where the Future Will Take Us

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Plant Genotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1245))

Abstract

Genetic diversity between individuals can be tracked and monitored using a range of molecular markers. These markers can detect variation ranging in scale from a single base pair up to duplications and translocations of entire chromosomal regions. The genotyping of individuals allows the detection of this variation and it has been successfully applied in plant science for many years. The increasing amounts of sequence data able to be generated using next-generation sequencing (NGS) technologies have produced a vast expansion in the rate of discovery of polymorphisms, with single nucleotide polymorphisms (SNPs) predominating as the marker of choice. This increase in polymorphic marker resources through efficient discovery, coupled with the utility of SNPs, has enabled the shift to high-throughput genotyping assays and these methods are reviewed and discussed here, alongside the recent innovations allowing increased throughput.

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References

  1. Mir RR, Varshney RK (2013) Future prospects of molecular markers in plants. In: Henry RJ (ed) Molecular markers in plants. Wiley, New York, pp 169–190

    Google Scholar 

  2. Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631

    Article  CAS  PubMed  Google Scholar 

  3. Makosiej A, Nasalski P, Giraud B, Vladimirescu A, Amara A (2008) An innovative sub-32nm SRAM current sense amplifier in double-gate CMOS insensitive to process variations and transistor mismatch. IEEE Int Conf Integr Circuit Design Technol Proc 2008:47–50

    Google Scholar 

  4. Lynch M, Milligan BG (1994) Analysis of population genetic-structure with RAPD markers. Mol Ecol 3:91–99

    Article  CAS  PubMed  Google Scholar 

  5. Appleby N, Edwards D, Batley J (2009) New technologies for ultra-high throughput genotyping in plants. In: Somers DJ, Langridge P, Gustafson JP (eds) Plant genomics. Humana, Kentucky, pp 19–40

    Chapter  Google Scholar 

  6. Kalia R, Rai M, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177: 309–334

    Article  CAS  Google Scholar 

  7. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed Central  PubMed  Google Scholar 

  8. Gu WK, Weeden NF, Yu J, Wallace DH (1995) Large-scale, cost-effective screening of PCR products in marker-assisted selection applications. Theor Appl Genet 91:465–470

    Article  CAS  PubMed  Google Scholar 

  9. Liu J, Huang SM, Sun MY, Liu SY, Liu YM, Wang WX, Zhang XR, Wang HZ, Hua W (2012) An improved allele-specific PCR primer design method for SNP marker analysis and its application. Plant Methods 8:34

    Article  CAS  PubMed Central  PubMed  Google Scholar 

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

    Chapter  Google Scholar 

  11. Giraud T, Enjalbert J, Fournier E, Delmotte F, Dutech C (2008) Population genetics of fungal diseases of plants. Parasite 15:449–454

    Article  CAS  PubMed  Google Scholar 

  12. Batley J, Edwards D (2007) SNP applications in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva H (eds) Association mapping in plants. Springer, New York, pp 95–102

    Chapter  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg GC, Edwards D (2007) BASC: an integrated bioinformatics system for Brassica research. Nucleic Acids Res 35:D870–D873

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Love CG, Batley J, Lim G, Robinson AJR, Savage D, Singh D, Spangenberg GC, Edwards D (2004) New computational tools for Brassica genome research. Comp Funct Genomics 5:276–280

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg GC, Edwards D (2005) Brassica ASTRA: an integrated database for Brassica genomic research. Nucleic Acids Res 33:W493–W495

    Article  PubMed Central  PubMed  Google Scholar 

  17. Love CG, Edwards D (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: Edwards D (ed) Plant bioinformatics. Humana Press, USA, pp 229–244

    Google Scholar 

  18. Edwards D, Batley J, Cogan NOI, Forster JW, Chagné D (2007) Single Nucleotide Polymorphism discovery. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva H (eds) Association mapping in plants. Springer, New York, pp 53–76

    Chapter  Google Scholar 

  19. Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D, Batley J (2012) SNP discovery and applications in Brassica napus. J Plant Biotechnol 39:1–12

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  21. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510

    Article  CAS  PubMed  Google Scholar 

  22. van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJT (2007) Complexity reduction of polymorphic sequences (CRoPS (TM)): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2:e1172

    Article  PubMed Central  PubMed  Google Scholar 

  23. Mammadov J, Chen W, Ren R, Pai R, Marchione W, Yalçin F, Witsenboer H, Greene T, Thompson S, Kumpatla S (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize (Zea mays L.) genome for use in marker-assisted breeding. Theor Appl Genet 121:577–588

    Article  CAS  PubMed  Google Scholar 

  24. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Zheng L, Bin L, Yan D, Nongyue H (2011) The state of field of high-throughput SNP genotyping system. In: Bioelectronics and bioinformatics (ISBB), 2011 international symposium, 3–5 Nov 2011, pp 174–177

    Google Scholar 

  26. Edenberg HJ, Liu Y (2009) Laboratory methods for high-throughput genotyping. Cold Spring Harbor Protoc 2009, pdb.top62

    Google Scholar 

  27. Bayés M, Gut IG (2011) Overview of genotyping. In: Rapley R, Harbron S (eds) Molecular analysis and genome discovery. John Wiley & Sons, Ltd, pp 1–23

    Chapter  Google Scholar 

  28. Fluidigm (2012) Biomark HD system. http://www.fluidigm.com/biomark-hd-system.html

  29. LifeTechnologies (2012) OpenArray® Real-Time PCR System. http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/real-time-pcr/real-time-pcr-instruments/openarray-real-time-pcr-system.html

  30. Biofire (2012) LightScanner® system mutation discovery, gene scanning and genotyping. biofire diagnostics. http://www.biofiredx.com/LightScanner/

  31. Tindall EA, Petersen DC, Nikolaysen S, Miller W, Schuster SC, Hayes VM (2010) Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Res Notes 3:39

    Article  PubMed Central  PubMed  Google Scholar 

  32. Durstewitz G, Polley A, Plieske J, Luerssen H, Graner EM, Wieseke R, Ganal MW (2010) SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus. Genome 53:948–956

    Article  CAS  PubMed  Google Scholar 

  33. Thudi M, Li YP, Jackson SA, May GD, Varshney RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 11:3–11

    Article  CAS  PubMed  Google Scholar 

  34. Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11:207

    Article  PubMed Central  PubMed  Google Scholar 

  35. Dai L, Xin G, Yan G, Jingfa X, Zhang Z (2012) Bioinformatics clouds for big data manipulation. Biol Direct 7:43

    Article  PubMed Central  PubMed  Google Scholar 

  36. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2–9

    Article  CAS  PubMed  Google Scholar 

  37. Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 10:609–618

    Article  CAS  PubMed  Google Scholar 

  38. Imelfort M, Batley J, Grimmond S, Edwards D (2009) Genome sequencing approaches and successes. In: Somers DJ, Langridge P, Gustafson JP (eds) Plant genomics. Humana, Kentucky, pp 345–358

    Chapter  Google Scholar 

  39. Lee HC, Lai KT, Lorenc MT, Imelfort M, Duran C, Edwards D (2012) Bioinformatics tools and databases for analysis of next-generation sequence data. Brief Funct Genomics 11:12–24

    Article  CAS  PubMed  Google Scholar 

  40. 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 

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Author information

Authors and Affiliations

  1. School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia

    Dhwani A. Patel, Manuel Zander, Jessica Dalton-Morgan & Jacqueline Batley

  2. Centre for Integrative Legume Research, University of Queensland, Brisbane, QLD, Australia

    Dhwani A. Patel, Manuel Zander, Jessica Dalton-Morgan & Jacqueline Batley

  3. School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia

    Jacqueline Batley

Authors
  1. Dhwani A. Patel
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  2. Manuel Zander
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  3. Jessica Dalton-Morgan
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  4. Jacqueline Batley
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Corresponding author

Correspondence to Jacqueline Batley .

Editor information

Editors and Affiliations

  1. School of Plant Biology, The University of Western Australia, Crawley, West Australia, Australia

    Jacqueline Batley

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Patel, D.A., Zander, M., Dalton-Morgan, J., Batley, J. (2015). Advances in Plant Genotyping: Where the Future Will Take Us. In: Batley, J. (eds) Plant Genotyping. Methods in Molecular Biology, vol 1245. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6_1

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  • DOI: https://doi.org/10.1007/978-1-4939-1966-6_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1965-9

  • Online ISBN: 978-1-4939-1966-6

  • eBook Packages: Springer Protocols

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