The allele-specific probe and primer amplification assay, a new real-time PCR method for fine quantification of single-nucleotide polymorphisms in pooled DNA

Applied and Environmental Microbiology

Volumn 78, Issue 4, 2012, Pages 1063-1068

  Billard, A ^a,b   Laval, V ^a   Fillinger, S ^a   Leroux, P ^a   Lachaise, H ^b   Beffa, R ^c   Debieu, D ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b BAYER AG   (Germany)

^c BAYER CROPSCIENCE AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLIFICATION CYCLES; AMPLIFICATION REFRACTORY MUTATION SYSTEMS; FALSE DISCOVERY RATE; FENHEXAMIDS; FUNGICIDE RESISTANCE; MANAGEMENT STRATEGIES; MICROBIOLOGICAL TESTS; MICROTITER PLATES; MINOR GROOVES; MONITORING METHODS; MUTATION ASSAYS; PHENYLALANINE RESIDUES; PLANT PATHOGEN; PRECISE METHOD; REAL-TIME PCR; REAL-TIME PCR METHOD; SINGLE-NUCLEOTIDE POLYMORPHISMS; STEROL BIOSYNTHESIS; TAQMAN PROBES;

AMINO ACIDS; ASSAYS; BIOCHEMISTRY; DNA; DNA SEQUENCES; FUNGICIDES; GENES; LAKES; PROBES;

POLYMERASE CHAIN REACTION;

AMIDE; FENHEXAMID; FUNGAL DNA; FUNGAL PROTEIN; FUNGICIDE; PRIMER DNA;

ALLELE; BIOASSAY; CHEMICAL BINDING; DNA; FUNGICIDE; INHIBITOR; MOLECULAR ANALYSIS; MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM; PROBE; QUANTITATIVE ANALYSIS; REAL TIME;

ALLELE; AMINO ACID SUBSTITUTION; ANTIFUNGAL RESISTANCE; ARTICLE; DRUG EFFECT; EVALUATION; FUNGUS; GENETICS; METHODOLOGY; MICROBIOLOGY; MISSENSE MUTATION; MYCOLOGY; PLANT DISEASE; REAL TIME POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; AMIDES; AMINO ACID SUBSTITUTION; DNA PRIMERS; DNA, FUNGAL; DRUG RESISTANCE, FUNGAL; FUNGAL PROTEINS; FUNGI; FUNGICIDES, INDUSTRIAL; MUTATION, MISSENSE; MYCOLOGY; PLANT DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84857098554     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06957-11     Document Type: Article

References (22)

1. Abbas A, Lepelley M, Lechevrel M, Sichel F. 2004. Assessment of DHPLC usefulness in the genotyping of GSTP1 exon 5 SNP: comparison to the PCR-RFLP method. J. Biochem. Biophys. Methods 59:121-126.
2. Amselem J, et al. 2011. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 7:e1002230.
3. Breen G, Harold D, Ralston S, Shaw D, St. Clair D. 2000. Determining SNP allele frequencies in DNA pools. Biotechniques 28:464-466.
4. Büttner P, et al. 1994. Variations in ploidy among isolates of Botrytis cinerea: implications for genetic and molecular analyses. Curr. Genet. 25: 445-450.
5. Debieu D, Bach J, Hugon M, Malosse C, Leroux P. 2001. The hydroxyanilide fenhexamid, a new sterol biosynthesis inhibitor fungicide efficient against the plant pathogenic fungus Botryotinia fuckeliana (Botrytis cinerea). Pest Manag. Sci. 57:1060-1067.
6. Dellaporta SL, Wood J, Hicks JB. 1983. A plant DNA minipreparation: version 2. Plant Mol. Biol. Rep. 1:19-21.
7. Fillinger S, et al. 2008. Genetic analysis of fenhexamide-resistant field isolates of the phytopathogenic fungus Botrytis cinerea. Antimicrob. Agents Chemother. 52:3933-3940.
8. Fraaije BA, Butters JA, Coelho JM, Jones DR, Hollomon DW. 2002. Following the dynamics of strobilurin resistance in Blumeria graminis f. sp. tritici using quantitative allele-specific real-time PCR measurements with the fluorescent dye SYBR green I. Plant Pathol. 51:45-54.
9. Germer S, Holland MJ, Higuchi R. 2000. High-throughput SNP allelefrequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10:258-266.
10. Glaab WE, Skopek TR. 1999. A novel assay for allelic discrimination that combines the fluorogenic 5' nuclease polymerase chain reaction (TaqMan) and mismatch amplification mutation assay. Mutat. Res. 430: 1-12.
11. Gruber JD, Colligan PB, Wolford JK. 2002. Estimation of single nucleotide polymorphism allele frequency inDNApools by using pyrosequencing. Hum. Genet. 110:395-401.
12. Kurg A, et al. 2000. Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet. Testing 4:1-7.
13. Leroux P, et al. 2002. The hydroxyanilide botryticide fenhexamid/mode of action and mechanism of resistance, p. 29-40. In Dehne HW, Gisi U, Kuck KH, Russel PE, and Lyr H (ed.), Modern fungicides and antifungal compounds III. AgroConcept GmbH, Bonn, Germany.
14. Ma Z, Michailides TJ. 2005. Advances in understanding molecular mechanisms of fungicide resistance and molecular detection of resistant genotypes in phytopathogenic fungi. Crop Prot. 24:853-863.
15. Ma Z, Michailides TJ. 2004. A real-time PCR assay for the detection of azoxystrobin-resistant Alternaria populations from pistachio orchards in California. Crop Prot. 23:1259-1263.
16. Mattarucchi E, et al. 2005. Different real time PCR approaches for the fine quantification of SNP's alleles in DNA pools: assays development, characterization and pre-validation. J. Biochem. Mol. Biol. 38:555-562.
17. Meletiadis J, Meis JF, Mouton JW, Verweij PE. 2001. Analysis of growth characteristics of filamentous fungi in different nutrient media. J. Clin. Microbiol. 39:478-484.
18. Moller EM, Bahnweg G, Sandermann H, Geiger HH. 1992. A simple and efficient protocol for isolation of high-molecular-weight DNA from filamentous fungi, fruit bodies, and infected-plant tissues. Nucleic Acids Res. 20:6115-6116.
19. Qin WJ, Yung LY. 2007. Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity. Nucleic Acids Res. 35:e111.
20. Rudi K, Zimonja M, Hannevik SE, Dromtorp SM. 2006. Multiplex real-time single nucleotide polymorphism detection and quantification by quencher extension. Biotechniques 40:323-329.
21. Skopek TR, Glaab WE, Monroe JJ, Kort KL, Schaefer W. 1999. Analysis of sequence alterations in a defined DNA region: comparison of temperature-modulated heteroduplex analysis and denaturing gradient gel electrophoresis. Mutat. Res. 430:13-21.
22. Yin JQ, Zhao RC, Morris KV. 2008. Profiling microRNA expression with microarrays. Trends Biotechnol. 26:70-76.