Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

Title
Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis
Publication Date
2005
Author(s)
Kerr, Richard John
McLachlan, G. M.
Henshall, John Mckeown
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
INRA, EDP Sciences
Place of publication
France
DOI
10.1186/1297-9686-37-1-83
UNE publication id
une:3156
Abstract
QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.
Link
Citation
Genetics Selection Evolution, 37(1), p. 83-103
ISSN
1297-9686
0999-193X
Start page
83
End page
103

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