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Chinese Science Bulletin

, Volume 56, Issue 24, pp 2523–2530 | Cite as

Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model

  • Gang He
  • Kang Huang
  • SongTao Guo
  • WeiHong Ji
  • XiaoGuang Qi
  • Yi Ren
  • XueLin Jin
  • BaoGuo Li
Open Access
Article Special Topic Conservation Biology of Endangered Wildlife

Abstract

Molecular studies using trace DNA, such as from museum specimens, ancient or forensic samples and samples obtained noninvasively, often have a common problem of low quality of DNA templates. Amplification errors, such as allelic dropout and false allele, may arise during polymerase chain reaction (PCR) using such samples. A mathematical model which treats homozygotes and heterozygotes discriminately has been developed to measure sample quality and compute the confidence level of using multiple-tube approaches. We use plucked hair samples collected from 26 individual Sichuan snub-nosed monkeys (Rhinopithecus roxellana) to test the model. In this case, a confidence level of 99% can be achieved by three positive PCRs. If the sample quality is very poor and requires many PCR replicates, an alternative multiple-step genotyping method is recommended. This model enables researchers to optimize experimental protocols through pilot studies and obtain reliable genetic information using noninvasive sampling method.

Keywords

Sichuan snub-nosed monkey noninvasive sampling microsatellite genotyping errors polynomial distribution model 

Supplementary material

11434_2011_4634_MOESM1_ESM.pdf (376 kb)
Supplementary material, approximately 375 KB.
11434_2011_4634_MOESM1_ESM.zip (170 kb)
Supplementary material, approximately 170 KB.

References

  1. 1.
    Woodruff D S. Non-invasive genotyping of primates. Primates, 1993, 34: 333–346CrossRefGoogle Scholar
  2. 2.
    Taberlet P, Luikart G. Noninvasive genetic sampling and individual identification. Biol J Linn Soc, 1999, 68: 41–55CrossRefGoogle Scholar
  3. 3.
    Gagneux P, Boesch C, Woodruff D S. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Mol Ecol, 1997, 6: 861–868CrossRefGoogle Scholar
  4. 4.
    Bradley B J, Boesch C, Vigilant L. Identification and redesign of human microsatellite markers for genotyping wild chimpanzee (Pan troglodytes verus) and gorilla (Gorilla gorilla gorilla) DNA from faeces. Conserv Genet, 2000, 1: 289–292CrossRefGoogle Scholar
  5. 5.
    Regnaut S, Lucas F S, Fumagalli L. DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations. Conserv Genet, 2006, 7: 449–453CrossRefGoogle Scholar
  6. 6.
    Hajibabaei M, Smith M, Janzen D H, et al. A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes, 2006, 6: 959–964CrossRefGoogle Scholar
  7. 7.
    Sefc K M, Payne R B, Sorenson M D. Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity. Conserv Genet, 2007, 8: 879–884CrossRefGoogle Scholar
  8. 8.
    Cooper A, Wayne R. New uses for old DNA. Curr Opin Biotech, 1998, 9: 49–53CrossRefGoogle Scholar
  9. 9.
    Park M J, Lee H Y, Chung U, et al. Y-STR analysis of degraded DNA using reduced-size amplicons. Int J Legal Med, 2007, 121: 152–157CrossRefGoogle Scholar
  10. 10.
    Taberlet P, Griffin S, Goossens B, et al. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res, 1996, 24: 3189–3194CrossRefGoogle Scholar
  11. 11.
    Morin P A, Chambers K E, Boesch C, et al. Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol Ecol, 2001, 10: 1835–1844CrossRefGoogle Scholar
  12. 12.
    Alonso A, Martín P, Albarrán C, et al. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci Int, 2004, 139: 141–149CrossRefGoogle Scholar
  13. 13.
    Navidi W, Arnheim N, Waterman M S. A multiple-tube approach for accurate genotyping of very small DNA samples by using PCR: Statistical considerations. Am J Hum Genet, 1992, 50: 347–359Google Scholar
  14. 14.
    Fernando P, Vidya T N C, Rajapakse C, et al. Reliable noninvasive genotyping: Fantasy or reality? J Hered, 2003, 94: 115–123CrossRefGoogle Scholar
  15. 15.
    Schlötterer C, Tautz D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res, 1992, 20: 211–215CrossRefGoogle Scholar
  16. 16.
    Foucault F, Praz F, Jaulin C, et al. Experimental limits of PCR analysis of (CA)n repeat alterations. Trends Genet, 1996, 12: 450–452CrossRefGoogle Scholar
  17. 17.
    Miller C R, Joyce P, Waits L P. Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics, 2002, 160: 357–366Google Scholar
  18. 18.
    Frantz A C, Pope L C, Carpenter P J, et al. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol Ecol, 2003, 12: 1649–1661CrossRefGoogle Scholar
  19. 19.
    Hansen H, Ben-David M, McDonald D B. Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their feces. Mol Ecol Resour, 2008, 8: 282–289CrossRefGoogle Scholar
  20. 20.
    Arandjelovic M, Guschanski K, Schubert G, et al. Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Mol Ecol Resour, 2009, 9: 28–36CrossRefGoogle Scholar
  21. 21.
    Ball M C, Pither R, Manseau M, et al. Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumption of low-quality and quantity template. Conserv Genet, 2007, 8: 577–586CrossRefGoogle Scholar
  22. 22.
    Miquel C, Bellemain E, Poillot C, et al. Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple-tube approach. Mol Ecol Notes, 2006, 6: 985–988CrossRefGoogle Scholar
  23. 23.
    Goossens B, Waits L P, Taberlet P. Plucked hair samples as a source of DNA: Reliability of dinucleotide microsatellite genotyping. Mol Ecol, 1998, 7: 1237–1241CrossRefGoogle Scholar
  24. 24.
    IUCN. IUCN Red List of Threatened Species. Version 2010.4. 2010. http://www.iucnredlist.org
  25. 25.
    Li B G, He P J, Yang X Z, et al. The present status of the Sichuan snub-nosed monkey in the Qinling Mountains of China, and a proposed conservation strategy for the species. Biosphere Conserv, 2001, 3: 107–114Google Scholar
  26. 26.
    Pan D, Li Y, Hu H X, et al. Microsatellite polymorphisms of Sichuan golden monkeys. Chinese Sci Bull, 2005, 50: 2850–2855CrossRefGoogle Scholar
  27. 27.
    He L, Zhang Y G, Li D Q, et al. Analysis on mitochondrial DNA D-loop sequences genetic polymorphism of Rhinopithecus roxellana (in Chinese). Chin J Zool, 2010, 1: 70–76Google Scholar
  28. 28.
    Guo S T, Ji W H, Li M, et al. The mating system of the Sichuan snub-nosed monkey (Rhinopithecus roxellana). Am J Primatol, 2010, 72: 25–32CrossRefGoogle Scholar
  29. 29.
    Guo S T. Inbreeding avoidance, paternity exclusion and matting system of Sichuan snub-nosed monkey in Qinling, China (in Chinese). Doctor Dissertation. Xi’an: Northwest University, 2007Google Scholar
  30. 30.
    Liu Z J, Ren B P, Hao Y L, et al. Identification of 13 human microsatellite markers via cross-species amplification of fecal samples from Rhinopithecus bieti. Int J Primatol, 2008, 29: 265–272CrossRefGoogle Scholar
  31. 31.
    Allen M, Engström A S, Meyers S, et al. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: Sensitivity and matching probabilities. J Forensic Sci, 1998, 43: 453–464Google Scholar
  32. 32.
    Zhang H, Li J H, Zhao J Y, et al. Morphological characters and genetic polymorphism analysis by microsatellite loci in Rhesus monkey stock from Wannan Mountains (in Chinese). Lab Anim Comparative Med, 2008, 28: 225–229Google Scholar
  33. 33.
    Rogers J, Garcia R, Shelledy W, et al. An initial genetic linkage map of the rhesus macaque (Macaca mulatta) genome using human microsatellite loci. Genomics, 2006, 87: 30–38CrossRefGoogle Scholar
  34. 34.
    Viguera E, Canceill D, Ehrlich S D. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J, 2001, 20: 2587–2595CrossRefGoogle Scholar
  35. 35.
    Primmer C R, Ellegren H. Patterns of molecular evolution in avian microsatellites. Mol Biol Evol, 1998, 15: 997–1008CrossRefGoogle Scholar
  36. 36.
    Whittaker J C, Harbord R M, Boxall N, et al. Likelihood-based estimation of microsatellite mutation rates. Genetics, 2003, 164: 781–787Google Scholar
  37. 37.
    Sainudiin R, Durrett R T, Aquadro C F, et al. Microsatellite mutation models, insights from a comparison of humans and chimpanzees. Genetics, 2004, 168: 383–395CrossRefGoogle Scholar
  38. 38.
    Leclercq S, Rivals E, Jarne P. DNA slippage occurs at microsatellite loci without minimal threshold length in humans: A comparative genomic approach. Genome Biol Evol, 2010, 2: 325–335CrossRefGoogle Scholar
  39. 39.
    Prugh L R, Ritland C E, Arthur S M, et al. Monitoring coyote population dynamics by genotyping faeces. Mol Ecol, 2005, 14: 1585–1596CrossRefGoogle Scholar
  40. 40.
    Constable J L, Ashley M V, Goodall J, et al. Noninvasive paternity assignment in Gombe chimpanzees. Mol Ecol, 2001, 10: 1279–1300CrossRefGoogle Scholar
  41. 41.
    Cai T T. One-sided confidence intervals in discrete distributions. J Stat Plann Infer, 2005, 131: 63–88CrossRefGoogle Scholar

Copyright information

© Science China Press and Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  1. 1.Key Laboratory of Resource Biology and Biotechnology in Western China of Ministry of Education, College of Life SciencesNorthwest UniversityXi’anChina
  2. 2.Ecology & Conservation Group, Institute for Natural SciencesMassey UniversityAucklandNew Zealand
  3. 3.Institute of ZoologyShaanxi Academy of SciencesXi’anChina
  4. 4.Shaanxi Wild Animal Rescue and Research CenterXi’anChina

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