Nonspecific PCR amplification by high-fidelity polymerases: Implications for next-generation sequencing of AFLP markers

Molecular Ecology Resources

Volumn 12, Issue 1, 2012, Pages 123-127

  Brelsford, Alan ^a   Collin, Hélène ^a   Perrin, Nicolas ^a   Fumagalli, Luca ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

454; Oryza sativa; Phoxinus phoxinus; Population genomics; SNP discovery

Indexed keywords

DNA DIRECTED DNA POLYMERASE; TAQ POLYMERASE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; ARTICLE; COMPARATIVE STUDY; CYPRINIFORMES; GENE LIBRARY; GENETICS; INSTRUMENTATION; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION; RICE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; CYPRINIDAE; DNA-DIRECTED DNA POLYMERASE; GENE LIBRARY; ORYZA SATIVA; POLYMERASE CHAIN REACTION; TAQ POLYMERASE;

ORYZA SATIVA; PHOXINUS PHOXINUS;

EID: 83955165922     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03063.x     Document Type: Article

References (23)

1. Andolfatto P, Davison D, Erezyilmaz D et al. (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Research, 21, 610-617.
2. Baird NA, Etter PD, Atwood TS et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3, e3376.
3. Bentley DR, Balasubramanian S, Swerdlow HP et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
4. Cha RS, Tilly WG (1993) Specificity, efficiency, and fidelity of PCR. Genome Research, 3, 518-529.
5. Cheung F, Haas BJ, Goldberg SMD et al. (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 life sciences technology. BMC Genomics, 7, 272.
6. Chou Q, Russel M, Birch DE, Raymond J, Bloch W (1992) Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucleic Acids Research, 20, 1717-1723.
7. Cline J, Braman JC, Hogrefe HH (1996) PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Research, 24, 3546-3551.
8. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
9. 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.
10. Gale JM, Tafoya GB (2004) Evaluation of 15 polymerases and phosphorothioate primer modification for detection of UV-induced C:G to T:A mutations by allele-specific PCR. Photochemistry and Photobiology, 79, 461-469.
11. Gompert Z, Forister ML, Fordyce JA et al. (2010) Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies. Molecular Ecology, 19, 2455-2473.
12. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
13. Kwok S, Chang S-Y, Sninsky JJ, Wang A (1994) A guide to the design and use of mismatched and degenerate primers. Genome Research, 3, 539-547.
14. Leroux S, Feve K, Vignoles F et al. (2010) Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing. BMC Research Notes, 3, 214.
15. Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics, 166, 351-372.
16. Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding, and 454-pyroseqeuncing in Amaranth. The Plant Genome, 2, 260-270.
17. Meudt HM, Clarke AC (2007) Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends in Plant Science, 12, 106-117.
18. Naghibalhossaini F, Moaddeb A (2006) An improved PCR-based amplification of unknown homologous DNA sequences. Biomolecular Engineering, 23, 209-212.
19. de Noronha CMC, Mullins JI (1992) Amplimers with 3′-terminal phosphorothioate linkages resist degradation by Vent polymerase and reduce Taq polymerase mispriming. Genome Research, 2, 131-136.
20. van Orsouw NJ, Hogers RCJ, Janssen A et al. (2007) Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One, 2, e1172.
21. van Tassell CP, Smith TPL, Matukumalli LK et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods, 5, 247-252.
22. Vos P, Hogers R, Bleeker M et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.
23. Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF (2010) SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genetics, 11, 32.