IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v78y2010i2p109-117.html
   My bibliography  Save this article

Reconstruction of pedigrees in clonal plant populations

Author

Listed:
  • Riester, Markus
  • Stadler, Peter F.
  • Klemm, Konstantin

Abstract

We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.

Suggested Citation

  • Riester, Markus & Stadler, Peter F. & Klemm, Konstantin, 2010. "Reconstruction of pedigrees in clonal plant populations," Theoretical Population Biology, Elsevier, vol. 78(2), pages 109-117.
    • Handle: RePEc:eee:thpobi:v:78:y:2010:i:2:p:109-117
    DOI: 10.1016/j.tpb.2010.05.002
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580910000456
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2010.05.002?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Cowell, Robert G., 2009. "Efficient maximum likelihood pedigree reconstruction," Theoretical Population Biology, Elsevier, vol. 76(4), pages 285-291.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Almudevar, Anthony & LaCombe, Jason, 2012. "On the choice of prior density for the Bayesian analysis of pedigree structure," Theoretical Population Biology, Elsevier, vol. 81(2), pages 131-143.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Cowell, Robert G., 2013. "A simple greedy algorithm for reconstructing pedigrees," Theoretical Population Biology, Elsevier, vol. 83(C), pages 55-63.
    2. Almudevar, Anthony, 2016. "An information theoretic approach to pedigree reconstruction," Theoretical Population Biology, Elsevier, vol. 107(C), pages 52-64.
    3. Sun, M. & Jobling, M.A. & Taliun, D. & Pramstaller, P.P. & Egeland, T. & Sheehan, N.A., 2016. "On the use of dense SNP marker data for the identification of distant relative pairs," Theoretical Population Biology, Elsevier, vol. 107(C), pages 14-25.
    4. Almudevar, Anthony & LaCombe, Jason, 2012. "On the choice of prior density for the Bayesian analysis of pedigree structure," Theoretical Population Biology, Elsevier, vol. 81(2), pages 131-143.
    5. Sheehan, Nuala A. & Bartlett, Mark & Cussens, James, 2014. "Improved maximum likelihood reconstruction of complex multi-generational pedigrees," Theoretical Population Biology, Elsevier, vol. 97(C), pages 11-19.
    6. Anderson, Eric C. & Ng, Thomas C., 2016. "Bayesian pedigree inference with small numbers of single nucleotide polymorphisms via a factor-graph representation," Theoretical Population Biology, Elsevier, vol. 107(C), pages 39-51.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:thpobi:v:78:y:2010:i:2:p:109-117. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.