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https://hdl.handle.net/1959.11/892
Title: | Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices | Contributor(s): | Meyer, K (author); Kirkpatrick, M (author) | Publication Date: | 2005 | Open Access: | Yes | DOI: | 10.1051/gse:2004034 | Handle Link: | https://hdl.handle.net/1959.11/892 | Abstract: | Principal component analysis is a widely used 'dimension reduction' technique, albeit generally at a phenotypic level. It is shown that we can estimate genetic principal components directly through a simple reparameterisation of the usual linear, mixed model. This is applicable to any analysis fitting multiple, correlated genetic effects, whether effects for individual traits or sets of random regression coefficients to model trajectories. Depending on the magnitude of genetic correlation, a subset of the principal component generally suffices to capture the bulk of genetic variation. Corresponding estimates of genetic covariance matrices are moreparsimonious, have reduced rank and are smoothed, with the number of parameters required to model the dispersion structure reduced from 'k'('k' + 1)/2 to 'm'(2'k' − 'm' + 1)/2 for 'k' effects and 'm' principal components. Estimation of these parameters, the largest eigenvalues and pertaining eigenvectors of the genetic covariance matrix, 'via' restricted maximum likelihood using derivatives of the likelihood, is described. It is shown that reduced rank estimation can reduce computational requirements of multivariate analyses substantially. An application to the analysis of eight traits recorded 'via' live ultrasound scanning of beef cattle is given. | Publication Type: | Journal Article | Source of Publication: | Genetics Selection Evolution, 37(1), p. 1-30 | Publisher: | INRA, EDP Sciences | Place of Publication: | France | ISSN: | 1297-9686 0999-193X |
Fields of Research (FoR) 2008: | 070201 Animal Breeding | Peer Reviewed: | Yes | HERDC Category Description: | C1 Refereed Article in a Scholarly Journal |
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Appears in Collections: | Animal Genetics and Breeding Unit (AGBU) Journal Article |
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open/SOURCE01.pdf | Publisher version (open access) | 206.8 kB | Adobe PDF Download Adobe | View/Open |
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