Multi-trait mixed models for QTL mapping in animal breeding typically are used with unstructured variance-covariance (VCOV) matrices for residual genetic effects. Even with few traits, with such a choice for the VCOV structure convergence problems and excessive time demands can occur. To remedy these problems some structuring of the VCOV is necessary. We propose to use factor analytic VCOV structures that were recently introduced in plant breeding. Factor analytic VCOV structures combine high flexibility with parsimonious use of parameters. We illustrate how factor analytic VCOV structures can efficiently be used in genome scans for QTL identification by means of an example from plant breeding in which we analyse 20 traits simultaneously.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 25.04, 2006
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