From genes to phenotypes - Evaluation of two methods for the SNP analysis in archaeological remains: Pyrosequencing and competitive allele specific PCR (KASPar)

Annals of Anatomy

Volumn 194, Issue 1, 2012, Pages 74-81

  Pruvost, Melanie ^a,b   Reissmann, Monika ^c   Benecke, Norbert ^b   Ludwig, Arne ^a  

^a LEIBNIZ INSTITUTE FOR ZOO AND WILDLIFE RESEARCH   (Germany)

^b GERMAN ARCHAEOLOGICAL INSTITUTE   (Germany)

^c HUMBOLDT UNIVERSITY   (Germany)

Author keywords

Ancient DNA; Coat color; Horse; KASPar; Paleogenetics; Pyrosequencing; Single nucleotide polymorphisms; SNP

Indexed keywords

ANCIENT DNA; CELL NUCLEUS DNA; DNA; UNCLASSIFIED DRUG;

ALLELE; ANIMAL TISSUE; ANTIQUITY; ARCHEOLOGY; ARTICLE; BONE; COMPETITIVE ALLELE SPECIFIC POLYMERASE CHAIN REACTION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE; GENE AMPLIFICATION; GENOTYPE; HETEROZYGOTE; HORSE; INTERMETHOD COMPARISON; KIT GENE; MATP GENE; METHODOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; POLYMERASE CHAIN REACTION; PYROSEQUENCING; RUSSIAN FEDERATION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SLC36A1 GENE;

ALLELES; ANIMALS; ARCHAEOLOGY; BONE AND BONES; DNA; DNA PRIMERS; HAIR COLOR; HORSES; PHENOTYPE; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SIBERIA; SPECIMEN HANDLING;

EQUIDAE;

EID: 84855494640     PISSN: 09409602     EISSN: 16180402     Source Type: Journal    
DOI: 10.1016/j.aanat.2011.10.007     Document Type: Article

References (22)

1. Benecke N., Pruvost M., Weber C. Die Pferdeskelette aus dem skythischen Fürstengrabhügel von ArŽan 2 (Tuva, Westsibirien) - Archäozoologie und Molekulargenetik. Der skythenzeitliche Furstenkurgan ArŽan 2 in Tuva. Archaologie in Eurasien 26 (Mainz 2010) 2010, 249-255. K.V. čugunov, H. Parzinger, A. Nagler (Eds.).
2. Bunce M., Worthy T.H., Ford T., Hoppitt W., Willerslev E., Drummond A., Cooper A. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 2003, 425(6954):172-175.
3. Cieslak M., Reissmann M., Hofreiter M., Ludwig A. Colours of domestication. Biol. Rev. 2011, 86. 10.1111/j.1469-185X.2011.00177.x.
4. Cieslak M., Pruvost M., Benecke N., Hofreiter M., Morales A., Reißmann M., Ludwig A. Origin and history of mitochondrial DNA lineages in domestic horses. PLoS ONE 2010, 5:12.
5. Green R.E., Krause J., Briggs A.W., Maricic T., et al. A draft sequence of the Neandertal genome. Science 2010, 328(5979):710-722.
6. Higuchi R.G., Wrischnik L.A., Oakes E., George M., Tong B., Wilson A.C. Mitochondrial DNA of the extinct quagga: relatedness and extent of postmortem change. J. Mol. Evol. 1987, 25(4):283-287.
7. Jaenicke-Després V., Buckler E.S., Smith B.D., Gilbert M.T., Cooper A., Doebley J., Pääbo S. Early allelic selection in maize as revealed by ancient DNA. Science 2003, 302(5648):1206-1208.
8. Krause J., Dear P.H., Pollack J.L., Slatkin M., Spriggs H., Barnes I., Lister A.M., Ebersberger I., Pääbo S., Hofreiter M. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 2006, 439(7077):724-727.
9. Lalueza-Fox C., Römpler H., Caramelli D., Stäubert C., Catalano G., Hughes D., Rohland N., Pilli E., Longo L., Condemi S., de la Rasilla M., Fortea J., Rosas A., Stoneking M., Schöneberg T., Bertranpetit J., Hofreiter M. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 2007, 318(5855):1453-1455.
10. Ludwig A., Arndt U., Lippold S., Benecke N., Debus L., King T.L., Matsumura S. Tracing the first steps of American sturgeon pioneers in Europe. BMC Evol. Biol. 2008, 8:221.
11. Ludwig A., Pruvost M., Reissmann M., Benecke N., Brockmann G.A., Castaños P., Cieslak M., Lippold S., Llorente L., Malaspinas A.S., Slatkin M., Hofreiter M. Coat color variation at the beginning of horse domestication. Science 2009, 324(5926):485.
12. Noonan J.P., Hofreiter M., Smith D., Priest J.R., Rohland N., Rabeder G., Krause J., Detter J.C., Pääbo S., Rubin E.M. Genomic sequencing of Pleistocene cave bears. Science 2005, 309(5734):597-599.
13. Noonan J.P., Coop G., Kudaravalli S., Smith D., Krause J., Alessi J., Chen F., Platt D., Pääbo S., Pritchard J.K., Rubin E.M. Sequencing and analysis of Neanderthal genomic DNA. Science 2006, 314(5802):1113-1118.
14. Pääbo S., Poinar H., Serre D., Jaenicke-Despres V., Hebler J., Rohland N., Kuch M., Krause J., Vigilant L., Hofreiter M. Genetic analyses from ancient DNA. Annu. Rev. Genet. 2004, 38:645-679.
15. Parzinger, H., 2010. Der skythenzeitliche Fürstenkurgan ArŽan 2 in Tuva-Ergebnisse und weiterführende Betrachtungen. In: čugunov, K.V., Parzinger, H., Nagler, A. (Eds.) Der skythenzeitliche Fürstenkurgan ArŽan 2 in Tuva. Archäologie in Eurasien 26 (Mainz 2010), 303-329.
16. Rieder S., Taourit S., Mariat D., Langlois B., Guérin G. Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm. Genome 2001, 12(6):450-455.
17. Rieder S. Molecular tests for coat colours in horses. J. Anim. Breed. Genet. 2009, 126(6):415-424.
18. Rohland N., Hofreiter M. Ancient DNA extraction from bones and teeth. Nat. Protoc. 2007, 2:1756-1762.
19. Römpler H., Rohland N., Lalueza-Fox C., Willerslev E., Kuznetsova T., Rabeder G., Bertranpetit J., Schöneberg T., Hofreiter M. Nuclear gene indicates coat-color polymorphism in mammoths. Science 2006, 311:392-394.
20. Römpler H., Dear P.H., Krause J., Meyer M., Rohland N., Schöneberg T., Spriggs H., Stiller M., Hofreiter M. Multiplex amplification of ancient DNA. Nat. Protoc. 2006, 1:720-728.
21. Svensson E.M., Anderung C., Baubliene J., Persson P., Malmstrom H., Smith C., Vretemark M., Daugnora L., Gotherstrom A. Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. Anim. Genet. 2007, 38:378-383.
22. Workman C., Dalen L., Vartanyan S., Shapiro B., Kosintsev P., Sher A., Gotherstrom A., Barnes I. Population-level genotyping of coat colour polymorphism in woolly mammoth (Mammuthus primigenius). Quat. Sci. Rev. 2011, 10.1016/j.quascirev.2010.08.020.