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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bengra C, Mifflin TE, Khripin Y, Manunta P, Williams SM, Jose PA, Felder RA (2002) Genotyping of essential hypertension single-nucleotide polymorphisms by a homogeneous PCR method with universal energy transfer primers. Clin Chem 48:2131–2140
Bourguet D, Guillemaud T, Chevillon C, Raymond M (2004) Fitness costs of insecticide resistance in natural breeding sites of the mosquito Culex pipiens. Evolution 58:128–135
Brunel D, Froger N, Pelletier G (1999) Development of amplified consensus genetic markers (ACGM) in Brassica napus from Arabidopsis thaliana sequences of known biological function. Genome 42:387–402
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Drouaud J, Camilleri C, Bourguignon P-Y, Canaguier A, Berard A, Vezon D, Giancola S, Brunel D, Colot V, Prum B, Quesneville H, Mezard C (2006) Variation in crossing over rates across the chromosome 4 of Arabidopsis thaliana: evidence for the presence of meiotic recombination “hot spots”. Genome Res (in press)
Fourmann M, Barret P, Froger N, Baron C, Charlot F, Delourme R, Brunel D (2002) From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for construction of a gene map. Theor Appl Genet 105:1196–1206
Gut IG (2004) An overview of genotyping and single nucleotide polymorphisms (SNP). In: Rapley R, Harbron S (eds) Molecular analysis and genome discovery. Wiley, Chichester, pp 43–64
Haughn GW, Smith J, Mazur B, Somerville C (1988) Transformation with a mutant Arabidopsis acetolactate synthase gene renders tobacco resistant to sulfonylurea herbicides. Mol Gen Genet 211:266–271
Leyser HM, Lincoln CA, Timpte C, Lammer D, Turner J, Estelle M (1993) Arabidopsis auxin-resistance gene AXR1 encodes a protein related to ubiquitin-activating enzyme E1. Nature 364:161–164
Livak KJ (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 14:143–149
McKhann HI, Camilleri C, Berard A, Bataillon T, David JL, Reboud X, Le Corre V, Caloustian C, Gut IG, Brunel D (2004) Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J 38:193–202
Myakishev MV, Khripin Y, Hu S, Hamer DH (2001) High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res 11:163–169
Pusch W, Kraeuter KO, Froehlich T, Stalgies Y, Kostrzewa M (2001) Genotools SNP manager: a new software for automated high-throughput MALDI-TOF mass spectrometry SNP genotyping. Biotechniques 30:210–215
Ravel C, Praud S, Canaguier A, Dufour P, Giancola S, Balfourier F, Chalhoub B, Brunel D, Linossier L, Dardevet M, Beckert M, Rousset M, Murigneux A, Charmet G (2004) DNA sequence polymorphism and their application in bread wheat. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation for plant breeding. Eucarpia: Tulln, Austria, pp 177–181
Ross P, Hall L, Smirnov I, Haff L (1998) High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 16:1347–1351
Roux F, Gasquez J, Reboud X (2004) The dominance of the herbicide resistance cost in several Arabidopsis thaliana mutant lines. Genetics 166:449–460
Roux F, Giancola S, Durand S, Reboud X (2005) Building an experimental cline with Arabidopsis thaliana to estimate herbicide fitness cost. Genetics (in press)
Rychlik W, Spencer WJ, Rhoads RE (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 18:6409–6412
Saini HS, Shefferd M, Henry RJ (1999) Microwave extraction of total genomic DNA from barley grains for use in PCR. J Inst Brew 105:185–190
Sauer S, Lechner D, Berlin K, Plancon C, Heuermann A, Lehrach H, Gut IG (2000) Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 28:E100
Scheible WR, Eshed R, Richmond T, Delmer D, Somerville C (2001) Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants. Proc Natl Acad Sci USA 98:10079–10084
Schmid KJ, Sorensen TR, Stracke R, Torjek 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 13:1250–1257
Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166
Tost J, Gut IG (2002) Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom Rev 21:388–418
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134
Acknowledgements
We thank the Mark Lathrop and the members of the Technology Development group of Ivo G. Gut at the Centre National de Génotypage: D. Lechner, C. Besse, F. Boussicault, D. Derbala, J-G. Garnier, F. Mauger, J-A. Perrier, C. Plançon and V. Sourice. We also thank the Informatics group: N. Wiart and F. Dos-Santos. We thank Christine Mézard for providing data on success rates. Part of this study was supported by a grant to FR from Bayer Crop Sciences. Genotyping has been financed by AIP-INRA “Séquençage végétal et post-séquençage” as well as by INRA SPE projects.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by A. Charcosset
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Giancola, S., McKhann, H.I., Bérard, A. et al. Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor and TaqMan, in diploid and polyploid plants. Theor Appl Genet 112, 1115–1124 (2006). https://doi.org/10.1007/s00122-006-0213-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-006-0213-6