Abstract
The development of next-generation sequencing (NGS) methods has helped the emergence of single nucleotide polymorphism (SNP) as the marker of choice. The SNPs are becoming increasingly popular in view of their abundance, ease in discovery, and the extremely high-throughput SNP genotyping at relatively low cost per data point. High-throughput genotyping may be defined as simultaneous genotyping for few to several hundreds or thousands of markers in hundreds to thousands of individuals. A variety of SNP genotyping strategies have been developed, many of which are applicable to already identified SNP loci with known sequences of their flanking regions. A number of these methods have been designed for high to very-high-throughput SNP genotyping. These methods require moderate to considerable sophistication and expensive instrumentation, and most of them have been commercialized. Therefore, most of them are closed technologies available to the user through the genotyping systems offered by the concerned companies. In addition, several strategies have been developed for simultaneous identification and genotyping of SNP loci; these methods are based on new generation DNA sequencing technologies. The chief methods for high throughput genotyping of already known SNPs and those for simultaneous SNP discovery and genotyping are discussed in some detail in this chapter.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Altshuler D, Pollara VJ, Cowles CR et al (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407:513–516
Andolfatto P, Davison D, Erezyilmaz D et al (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21:610–617
Baird N, Etter P, Atwood T et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376
Catchen J, Hohenlohe PA, Bassham S et al (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140. doi:10.1111/mec.12354
Chudyk JP, Rusch TL, Fieweger KM et al (2006) Automating microsatellite genotyping with array tape. JALA 11:260–267
Davey JW, Blaxter ML (2010) RADSeq: next-generation population genetics. Brief Funct Genomics 9:416–423
Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Rev Genet 12:499–510
de Vienne D, Santoni S, Falque M (2003) Principal sources of molecular markers. In: de Vienne D (ed) Molecular markers in plant genetics and biotechnology. Science Publishers, Enfield, pp 3–46
Deschamps S, Campbell MA (2013) Genetic variant discovery and its use in genome characterization of ergonomically important crop species. In: Henry RJ (ed) Molecular markers in plants. Wiley, USA, pp 138–167
Elshire RJ, Glaubitz JC, Sun Q et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379
Fan J-B, Gunderson KL, Bibikova M et al (2006) Illumina universal bead arrays. Methods Enzymol 410:57–73
Glaubitz JC, Casstevens TM, Lu F et al (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9:e90346. doi:10.1371/journal.pone.0090346
Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18
Hoffmann TJ, Kvale MN, Hesselson SE et al (2011) Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 98:79–89
Ji H, Welch K (2009) Molecular inversion probe assay for allelic quantitation. Methods Mol Biol 556:67–87
Kahl G, Mast A, Tooke N et al (2005) Single nucleotide polymorphisms: detection techniques and their potential for genotyping and genome mapping. In: Meksem K, Kahl G (eds) The handbook of plant genome mapping, genetic and physical mapping. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 75–107
Kofler R, Orozco-ter Wengel P, De Maio N et al (2011) PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS ONE 6:e15925. doi:10.1371/journal.pone.0015925
Li H, Bradbury P, Ersoz E et al (2011a) Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS ONE 6:e17573. doi:10.1371/journal.pone.0017573
Li Y, Sidore C, Kang HM et al (2011b) Low-coverage sequencing: implications for design of complex trait association studies. Genome Res 21:94–951
Lin CH, Yeakley JM, McDaniel TK et al (2009) Medium- to high-throughput SNP genotyping using veracode microbeads. Methods Mol Biol 496:129–142
Lyamichev V, Mast AL, Hall JG et al (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nature Biotechnol 17:292–296
Mir RR, Varshney RK (2013) Future prospects of molecular markers in plants. In: Henry RJ (ed) Molecular markers in plants. Wiley, USA, pp 169–190
Peterson BK, Weber JN, Kay EH et al (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135. doi:10.1371/journal.pone.0037135
Poland JA, Brown PJ, Sorrells ME et al (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253. doi:10.1371/journal.pone.0032253
Rodi CP, Darnhofer-Patel B, Stanssens P et al (2002) A strategy for the rapid discovery of disease markers using the MassARRAY system. BioTechniques Suppl 32:S62–S69
Sonah H, Bastien M, Iquira E et al (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8:e54603. doi:10.1371/journal.pone.0054603
Thompson HJ, Zhao K, Wright M et al (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:875–886
Toonen RJ, Puritz JB, Forsman ZH et al (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1:e203. doi:10.7717/peerj.203
Tsuchihashi Z, Dracopoli NC (2002) Progress in high throughput SNP genotyping methods. Pharmacogenomics J 2:103–110
van Tassell CP, Smith TPL, Matukumalli LK et al (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252
vanOrsouw NJ, Hogers RCJ, Janssen A et al (2007) Complexity reduction of polymorphic sequences (CRoPSâ„¢): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172. doi:10.1371/journal.pone.0001172
Wang J, Lin M, Crenshaw A et al (2009a) High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics 10:561–573
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2015 Author(s)
About this chapter
Cite this chapter
Singh, B.D., Singh, A.K. (2015). High-Throughput SNP Genotyping. In: Marker-Assisted Plant Breeding: Principles and Practices. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2316-0_13
Download citation
DOI: https://doi.org/10.1007/978-81-322-2316-0_13
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2315-3
Online ISBN: 978-81-322-2316-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)