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United States Department of Agriculture

Agricultural Research Service

Title: Including Genetic Groups for Qtl Effects in Marker Assisted Selection

Authors
item Hanford, Kathryn
item Thallman, Richard
item Kachman, S. - UNIV. OF NEBR.-LINCOLN
item Van Vleck, Lloyd

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: June 1, 2004
Publication Date: July 26, 2004
Citation: Hanford, K.J., Thallman, R.M., Kachman, S.D., Van Vleck, L.D. 2004. Including genetic groups for QTL effects in marker assisted selection [abstract]. Journal of Animal Science 82(Suppl. 1):414.

Interpretive Summary: No interpretive summary is required.

Technical Abstract: Genetic group effects provide a means of accounting for the effect of selection that cannot be accounted for by records of relatives. In a polygenic animal model, genetic group effects are incorporated into the mixed model equations (MME) by adding one equation for each genetic group corresponding to foundation (phantom) animals. With minor modifications the rules for the inverse of the relationship matrix without genetic groups can be used to obtain the inverse of the coefficient matrix after absorption of the equations for the phantom animals needed for solving the MME. With identification of quantitative trait loci (QTL), information from closely linked genetic markers can be included in prediction of breeding values with mixed model equations to implement marker assisted selection (MAS), where effects of QTL alleles are considered random. As with the polygenic animal model, the distribution of the QTL alleles can be different within different subpopulations. Genetic group effects for the QTL may also arise from QTL effects that depend on the genetic background of the different subpopulations. Current methods for MAS with solutions from mixed model equations do not allow for incorporating genetic group effects for QTL. An extension has been developed which allows genetic group effects to be incorporated in the MME to obtain genetic evaluations for MAS by augmenting the MME by the number of genetic groups used in models without marker information. Rules for constructing the inverse of the QTL coefficient matrix after absorption of the equations for the phantom animals and augmenting the MME with this matrix have been derived and will be presented.

Last Modified: 10/25/2014
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