title: Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants.
abstract: The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor and TaqMan are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.
authors.affiliation: Station de Génétique et d'Amélioration des Plantes, INRA, Route de Saint Cyr, 78026 Versailles cedex, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Giancola
authors.forename: Heather I
authors.initials: HI
authors.lastname: McKhann
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.forename: Christine
authors.initials: C
authors.lastname: Camilleri
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Durand
authors.forename: Pierre
authors.initials: P
authors.lastname: Libeau
authors.forename: Fabrice
authors.initials: F
authors.lastname: Roux
authors.forename: Xavier
authors.initials: X
authors.lastname: Reboud
authors.forename: Ivo G
authors.initials: IG
authors.lastname: Gut
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029688:Brassica napus / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D004171:Diploidy; D005787:Gene Frequency; D005838:Genotype; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D018744:DNA, Plant