Pedigree-free animal models: The relatedness matrix reloaded

School of Integrative Biology, University of Queensland, St Lucia, Queensland 4072, Australia.
Proceedings of the Royal Society B: Biological Sciences (Impact Factor: 5.05). 04/2008; 275(1635):639-47. DOI: 10.1098/rspb.2007.1032
Source: PubMed


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.

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Available from: Terry Burke, Oct 06, 2015
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    • "Por este motivo, la exactitud de los estimativos de heredabilidad hallados con este método han sido cuestionados por varios autores (Bouvet et al. 2008, Garant y Kruuk 2005). Para varias poblaciones con conocimiento de la genealogía se estimó heredabilidad a través del método de Ritland y el método clásico, encontrando que en el primero los valores de heredabilidad son menos exactos comparados con el segundo (Coltman 2005, Frentiu et al. 2008, Thomas et al. 2002). Sin embargo, Bessega et al. (2009) encuentran una consistencia entre los estimativos de heredabilidad obtenidos por los métodos clásicos y a través del método de Ritland en la planta Prosopis alba, gracias a que en la población existe una varianza de parentesco significativa. "
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    • "For primates this is often a social pedigree of maternal links and paternities using parentage assignment based on molecular markers. Methods have been proposed to approximate A exclusively from molecular markers, though they have yet to receive wide use (Frentiu et al. 2008; Pemberton 2008; Sillanpää 2011). Additional random effects can be used to account for repeated observations on individuals and maternal effects (see later, and Wilson et al. 2010). "
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    • "These methods were based on linear relationships between markerbased estimates of relatedness and phenotypes. However, because of uncertainty in estimate of relatedness and confounding of relatedness with the environment, h 2 estimates from these methods have not been accurate (Coltman 2005; Frentiu et al. 2008; Pemberton 2008; Gay, Siol & Ronfort 2013). In recent years, multiple methods have been developed in the animal breeding literature that use large-scale genomic data to predict phenotypes (Meuwissen, Hayes & Goddard 2001; Van Raden 2008; Goddard et al. 2009; Campos et al. 2012) and estimate heritability based on the proportion of phenotypic variance explained by genotyped SNPs. "
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