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Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

Abstract

Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA) may provide an avenue for structuring (co)variance matrices, thus reducing the number of parameters needed for describing (co)dispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (co)variance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model.

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Correspondence to Gustavo de los Campos.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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de los Campos, G., Gianola, D. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation. Genet Sel Evol 39, 481 (2007). https://doi.org/10.1186/1297-9686-39-5-481

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  • DOI: https://doi.org/10.1186/1297-9686-39-5-481

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