Skip to main content
SpringerLink
Log in

SNP Genotyping Technologies

  • Chapter
  • First Online:
Diagnostics in Plant Breeding

Abstract

In the recent years, single nucleotide polymorphism (SNP) markers have emerged as the marker technology of choice for plant genetics and breeding applications. Besides the efficient technologies available for SNP discovery even in complex genomes, one of the main reasons for this is the availability of high-throughput platforms for multiplexed SNP genotyping. Advancements in these technologies have enabled increased flexibility and throughput, allowing for the generation of adequate SNP marker data at very competitive cost per data point.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8(11):554–560

    Article  PubMed  CAS  Google Scholar 

  • Bagge M, Lübberstedt T (2008) Functional markers in wheat: technical and economic aspects. Mol Breed 22(3):319–328

    Article  Google Scholar 

  • Bayes M, Gut IG (2011) Overview of genotyping. In: Rapley R, Harbron S (eds) Molecular analysis and genome discovery, 2nd edn. Wiley, Chichester, pp 1–19

    Chapter  Google Scholar 

  • Chagné D, Batley J, Edwards D, Forster JW (2007) Single nucleotide polymorphism genotyping in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, Silva HN (eds) Association mapping in plants. Springer, New York, pp 77–94

    Chapter  Google Scholar 

  • Choi I-Y, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon M-S, Hwang E-Y, Yi S-I, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176(1):685–696

    Article  PubMed  CAS  Google Scholar 

  • Collins DW, Jukes TH (1994) Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics 20(3):386–396

    Article  PubMed  CAS  Google Scholar 

  • 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(7):499–510

    Article  PubMed  CAS  Google Scholar 

  • De la Vega FM, Lazaruk KD, Rhodes MD, Wenz MH (2005) Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP genotyping assays and the SNPlex genotyping system. Mutat Res 573(1–2):111–135

    PubMed  Google Scholar 

  • Edward K, Poole R, Barker G (2008) SNP discovery in plants. In: Henry R (ed) Plant genotyping II SNP technology. CABI, Oxfordshire, pp 1–29

    Chapter  Google Scholar 

  • 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 

  • Ekstrom B, Alderborn A, Hammerling U (2000) Pyrosequencing for SNPs. Prog Biomed Opt Imaging 1:134–139

    Google Scholar 

  • Elshire RJ (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  PubMed  CAS  Google Scholar 

  • Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 68:69–78

    Article  PubMed  CAS  Google Scholar 

  • Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, Wickham Garcia E, Lebruska LL, Laurent M, Shen R, Barker D, Kimmel A, Oliver B (2006) Illumina universal bead arrays. In: Methods in enzymology, vol 410. Academic, San Diego, pp 57–73

    Google Scholar 

  • Grattapaglia D, Silva OB, Kirst M, de Lima BM, Faria DA, Pappas GJ (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol 11:65

    Article  PubMed  CAS  Google Scholar 

  • Gunderson KL, Steemers FJ, Ren H, Ng P, Zhou L, Tsan C, Chang W, Bullis D, Musmacker J, King C, Lebruska LL, Barker D, Oliphant A, Kuhn KM, Shen R (2006) Whole-genome genotyping. In: Alan K, Brian O (eds) Methods in enzymology, vol 410. Academic, San Diego, pp 359–376

    Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101(1):5–18

    Article  PubMed  CAS  Google Scholar 

  • Hamblin MT, Buckler ES, Jannink J-L (2011) Population genetics of genomics-based crop improvement methods. Trends Genet 27(3):98–106

    Article  PubMed  CAS  Google Scholar 

  • Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21(6):673–678

    Article  PubMed  CAS  Google Scholar 

  • Hardenbol P, Yu FL, 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 XH, Miao X, Moore B, Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang ZY, Jones HB, Davis RW, Willis TD, Gibbs RA (2005) Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 15(2):269–275

    Article  PubMed  CAS  Google Scholar 

  • Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155(2):645–655

    Article  PubMed  CAS  Google Scholar 

  • Holland PM, Abramson RD, Watson R, Gelfand DH (1991) Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA 88(16):7276–7280

    Article  PubMed  CAS  Google Scholar 

  • Holloway JW, Beghé B, Turner S, Hinks LJ, Day INM, Howell WM (1999) Comparison of three methods for single nucleotide polymorphism typing for DNA bank studies: sequence-specific oligonucleotide probe hybridisation, TaqMan liquid phase hybridisation, and microplate array diagonal gel electrophoresis (MADGE). Hum Mutat 14(4):340–347

    Article  PubMed  CAS  Google Scholar 

  • Huang X (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076

    Article  PubMed  CAS  Google Scholar 

  • International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449(7164):851–861

    Article  Google Scholar 

  • Jones ES, Sullivan D, Bhattramakki D, Smith JSC (2007) A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theor Appl Genet 115:361–371

    Article  PubMed  CAS  Google Scholar 

  • Kennedy GC, Matsuzaki H, Dong S, W-m L, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SPA, Jones KW (2003) Large-scale genotyping of complex DNA. Nat Biotechnol 21(10):1233–1237

    Article  PubMed  CAS  Google Scholar 

  • Kennedy B, Arar K, Reja V, Henry RJ (2006) Locked nucleic acids for optimizing displacement probes for quantitative real-time PCR. Anal Biochem 348(2):294–299

    Article  PubMed  CAS  Google Scholar 

  • Kurg A, Tõnisson N, Georgiou I, Shumaker J, Tollett J, Metspalu A (2000) Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet Test 4(1):1–7

    Article  PubMed  CAS  Google Scholar 

  • Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50(7):1156–1164

    Article  PubMed  CAS  Google Scholar 

  • Mammadov J, Chen W, Mingus J, Thompson S, Kumpatla S (2012) Development of versatile gene-based SNP assays in maize (Zea mays L.). Mol Breed 29(3):779–790

    Article  CAS  Google Scholar 

  • Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh PS, Jones KW, Fodor SPA, Mei R (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 1(2):109–111

    Article  PubMed  CAS  Google Scholar 

  • McGuigan FEA, Ralston SH (2002) Single nucleotide polymorphism detection: allelic discrimination using TaqMan. Psychiatr Genet 12(3):133–136

    Article  PubMed  Google Scholar 

  • Mhlanga MM, Malmberg L (2001) Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR. Methods 25(4):463–471

    Article  PubMed  CAS  Google Scholar 

  • Morrell LP, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13:85–96

    CAS  Google Scholar 

  • Nakahara H, Sekiguchi K, Hosono N, Kubo M, Takahashi A, Nakamura Y, Kasai K (2010) Criterion values for multiplex SNP genotyping by the invader assay. Forensic Sci Int Genet 4:130–136

    Article  PubMed  CAS  Google Scholar 

  • Nazar RN, Robb J (2011) DNA chip analysis in genome discovery. In: Rapley R, Harbron S (eds) Molecular analysis and genome discovery, 2nd edn. Wiley, Chichester, pp 24–37

    Chapter  Google Scholar 

  • Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17(7):2503–2516

    Article  PubMed  CAS  Google Scholar 

  • Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary B, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265(5181):2085–2088

    Article  PubMed  CAS  Google Scholar 

  • Olivier M (2005) The Invader® assay for SNP genotyping. Mutat Res 573:103–110

    Article  PubMed  CAS  Google Scholar 

  • Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci USA 86:2766–2770

    Article  PubMed  CAS  Google Scholar 

  • Pastinen T, Kurg A, Metspalu A, Peltonen L, Syvänen A-C (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res 7(6):606–614

    PubMed  CAS  Google Scholar 

  • Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30(5):1071–1088

    Article  PubMed  CAS  Google Scholar 

  • Perkel J (2008) SNP genotyping: six technologies that keyed a revolution. Nat Methods 5(5):447–453

    Article  CAS  Google Scholar 

  • Podder M, Ruan J, Tripp B, Chu Z, Tebbutt S (2008) Robust SNP genotyping by multiplex PCR and arrayed primer extension. BMC Med Genomics 1(1):5

    Article  PubMed  Google Scholar 

  • Ragoussis J (2009) Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 10(1):117–133

    Article  PubMed  CAS  Google Scholar 

  • Ragoussis J, Elvidge G (2006) Affymetrix GeneChip® system: moving from research to the clinic. Expert Rev Mol Diagn 6(2):145–152

    Article  PubMed  CAS  Google Scholar 

  • Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME (2006) Global variation in copy number in the human genome. Nature 444(7118):444–454

    Article  PubMed  CAS  Google Scholar 

  • Sauer S, Lechner D, Berlin K, Plançon C, Heuermann A, Lehrach H, Gut IG (2000) Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 28(23):e100

    Article  PubMed  CAS  Google Scholar 

  • Schmid KJ, Sörensen TR, Stracke R, Törjék O, Altmann T, Mitchell-Olds T, Weisshaar B (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13(6a):1250–1257

    Article  PubMed  Google Scholar 

  • Shen R, Fan J-B, Campbell D, Chang W, Chen J, Doucet D, Yeakley J, Bibikova M, Wickham Garcia E, McBride C, Steemers F, Garcia F, Kermani BG, Gunderson K, Oliphant A (2005) High-throughput SNP genotyping on universal bead arrays. Mutat Res 573(1–2):70–82

    PubMed  CAS  Google Scholar 

  • Shumaker JM, Metspalu A, Caskey CT (1996) Mutation detection by solid phase primer extension. Hum Mutat 7(4):346–354

    Article  PubMed  CAS  Google Scholar 

  • Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL (2006) Whole-genome genotyping with the single-base extension assay. Nat Methods 3(1):31–33

    Article  PubMed  CAS  Google Scholar 

  • Studer B, Jensen LB, Fiil A, Asp T (2009) “Blind” mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis. Mol Breed 24(2):191–199

    Article  CAS  Google Scholar 

  • Suharyanto S, Shiraishi S (2011) An identification system using multiplex allele-specific PCR assay in the Japanese black pine (Pinus thunbergii Parl.). Breed Sci 61(3):301–306

    Article  CAS  Google Scholar 

  • Syvanen A-C (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2(12):930–942

    Article  PubMed  CAS  Google Scholar 

  • Syvanen A-C (2005) Toward genome-wide SNP genotyping. Nat Genet 37:5–10

    Article  Google Scholar 

  • Tang K, Oeth P, Kammerer S, Denissenko MF, Ekblom J, Jurinke C, van den Boom D, Braun A, Cantor CR (2004) Mining disease susceptibility genes through SNP analyses and expression profiling using MALDI-TOF mass spectrometry. J Proteome Res 3(2):218–227

    Article  PubMed  CAS  Google Scholar 

  • Täpp I, Malmberg L, Rennel E, Wik M, Syvänen AC (2000) Homogeneous scoring of single-nucleotide polymorphisms: comparison of the 5′-nuclease TaqMan assay and Molecular Beacon probes. Biotechniques 28(4):732–738

    PubMed  Google Scholar 

  • Thompson JF, Milos PM (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12:217

    PubMed  CAS  Google Scholar 

  • Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu PP, Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De La Vega FM, Rhodes MD, Hennessy KM, Wenz HM (2005) The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Tech 16(4):398–406

    PubMed  Google Scholar 

  • Torjek O, Berger D, Meyer RC, Mussig C, Schmid KJ, Sorensen TR, Weisshaar B, Mitchell-Olds T, Altmann T (2003) Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J 36(1):122–140

    Article  PubMed  CAS  Google Scholar 

  • Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27(9):522–530

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Agricultural Sciences, Forage Crop Genetics, ETH Zurich, Universitätsstrasse 2, 8092, Zurich, Switzerland

    Bruno Studer

  2. Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046, Zurich, Switzerland

    Roland Kölliker

Authors
  1. Bruno Studer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Roland Kölliker
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bruno Studer .

Editor information

Editors and Affiliations

  1. Dept. Agronomy, Iowa State University, Agronomy Hall 1204, Ames, 50011, Iowa, USA

    Thomas Lübberstedt

  2. ICRISAT, Centre of Excellence in Genomics (CEG), Patancheru, 502 324, Andra Pradesh, India

    Rajeev K. Varshney

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Studer, B., Kölliker, R. (2013). SNP Genotyping Technologies. In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_9

Download citation

Publish with us

Policies and ethics

Search

Navigation