Factor-analytic models for genotype × environment type problems and structured covariance matrices.docVIP

Genetics Selection Evolution BioMedCentral Review Open Access Factor-analytic models for genotype × environment type problems and structured covariance matrices Karin Meyer Address: Animal Genetics and Breeding Unit, University of New England, Armidale, NSW 2351, Australia Email: Karin Meyer - kmeyer@.au Published: 30 January 2009 Received: 22 January 2009 Accepted: 30 January 2009 Genetics Selection Evolution 2009, 41:21 doi:10.1186/1297-9686-41-21 This article is available from: /content/41/1/21 ? 2009 Meyer; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Analysis of data on genotypes with different expression in different environments is a classic problem in quantitative genetics. A review of models for data with genotype × environment interactions and related problems is given, linking early, analysis of variance based formulations to their modern, mixed model counterparts. Results: It is shown that models developed for the analysis of multi-environment trials in plant breeding are directly applicable in animal breeding. In particular, the additive main effect, multiplicative interaction models accommodate heterogeneity of variance and are characterised by a factor-analytic covariance structure. While this can be implemented in mixed models by imposing such structure on the genetic covariance matrix in a standard, multi-trait model, an equivalent model is obtained by fitting the common and specific factors genetic separately. Properties of the mixed model equations for alternative implementations of factor-analytic models are discussed, and extensions to structured modelling of covariance matrices for multi-trait, multi-environment sce