Pedigree-free Animal Models: the Relatedness Matrix Reloaded

Frentiu, F., Clegg, S.M., Chittock, J., Burke, T., Blows, M. W. and Owens, I.P.F. (2008) Pedigree-free Animal Models: the Relatedness Matrix Reloaded. Proceedings of the Royal Society of London - B, 275 1635: 639-647. doi:10.1098/rspb.2007.1032


Author Frentiu, F.
Clegg, S.M.
Chittock, J.
Burke, T.
Blows, M. W.
Owens, I.P.F.
Title Pedigree-free Animal Models: the Relatedness Matrix Reloaded
Journal name Proceedings of the Royal Society of London - B   Check publisher's open access policy
ISSN 0962-8452
Publication date 2008-01-01
Sub-type Article (original research)
DOI 10.1098/rspb.2007.1032
Volume 275
Issue 1635
Start page 639
End page 647
Total pages 9
Place of publication United Kingdom
Publisher The Royal Society
Language eng
Subject C1
970106 Expanding Knowledge in the Biological Sciences
060303 Biological Adaptation
060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
Abstract Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance–covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland’s pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rank R matrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of the R matrix in order to maximize the signal to noise ratio. Using reduced-rank R matrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.
Keyword Quantitative Genetics
Animal Model
Relatedness
Molecular Markers
Morphology
Birds
Q-Index Code C1
Q-Index Status Confirmed Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
School of Biological Sciences Publications
 
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Created: Fri, 23 Jan 2009, 03:08:43 EST by Gail Walter on behalf of School of Biological Sciences