SNP Genotyping Technologies

Abstract

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Applied oilseed rape marker technology and genomics

“…Commonly applied marker types changed from hybridization-based markers analysed by gel electrophoresis in the 1980s to PCR-based markers analysed initially by gel electrophoresis and later by fluorescence detection in the 1990s up to more sophisticated highly parallel multi-enzyme-and multi-fluorescence detection-based genotypingby-hybridization and GBS approaches in the last decade (Table 16.2, for details on marker technologies applied to B. napus also see reviews in Gail and Sharpe, 2012;Studer and Kölliker, 2013;Mir et al, 2014). Commonly applied marker types changed from hybridization-based markers analysed by gel electrophoresis in the 1980s to PCR-based markers analysed initially by gel electrophoresis and later by fluorescence detection in the 1990s up to more sophisticated highly parallel multi-enzyme-and multi-fluorescence detection-based genotypingby-hybridization and GBS approaches in the last decade (Table 16.2, for details on marker technologies applied to B. napus also see reviews in Gail and Sharpe, 2012;Studer and Kölliker, 2013;Mir et al, 2014).…”

“…In commercial breeding, SSR markers are up to this day still commonly used in many genotyping applications including MAS in B. napus (Table 16.6). HRM can be used for genotyping of SNPs and other polymorphisms (Studer and Kölliker, 2013). HRM can be used for genotyping of SNPs and other polymorphisms (Studer and Kölliker, 2013).…”

“…Initially, enzyme-based genotyping-byhybridization assays allowing medium throughput were developed, e.g. The KASP (KASPar) assays provided by the company KBioScience/LGC Genomics since 2005 (Cuppen, 2007, Semagn et al, 2014) is a slightly modified method to the TaqMan method using a unique form of allele-specific PCR (Studer and Kölliker, 2013). The TaqMan assay is based on the 5 0 exonuclease activity of the Taq polymerase and the use of allele-specific probes coupled to a quencher molecule and a fluorescent dye.…”

“…These SNP assays are based on single base primer extension or oligonucleotide ligation with fluorescently labelled nucleotides and capillary gel electrophoresis (Studer and Kölliker, 2013). These SNP assays are based on single base primer extension or oligonucleotide ligation with fluorescently labelled nucleotides and capillary gel electrophoresis (Studer and Kölliker, 2013).…”

“…It exploits the steep decrease in costs for next-generation sequencing (NGS) technologies in the last years (Snowdon and Iniguez-Luy, 2012;Studer and Kölliker, 2013) and will clearly become the marker genotyping platform of choice in the coming years (Mir and Varshney, 2013). It exploits the steep decrease in costs for next-generation sequencing (NGS) technologies in the last years (Snowdon and Iniguez-Luy, 2012;Studer and Kölliker, 2013) and will clearly become the marker genotyping platform of choice in the coming years (Mir and Varshney, 2013).…”