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United States Department of Agriculture

Agricultural Research Service

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Approximation of reliability of direct genomic breeding values

Authors
item Sargolzaei, Mehdi -
item Schaeffer, Larry -
item Chesnais, Jacques -
item Kistemaker, Gerrit -
item WIGGANS, GEORGE
item Schenkel, Flavio -

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: April 21, 2014
Publication Date: August 17, 2014
Citation: Sargolzaei, M., Schaeffer, L.R., Chesnais, J., Kistemaker, G., Wiggans, G.R., Schenkel, F.S. 2014. Approximation of reliability of direct genomic breeding values. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.

Technical Abstract: Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first method is based on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationship with the individual of interest. The second method is a ridge-regression method for which the direct inverse of LHS for a small subset of SNP is required. The performance of the proposed methods was investigated for the North American genomic data set, consisting of 228,168 genotyped individuals. The ridge-regression method results in very high correlations between theoretical and estimated reliabilities for subsets of 5k SNP and above. It is easily applicable to large data sets. Both methods lead to some biases in the mean and SD of reliabilities but these can be corrected by pegging to theoretical values or values from validation studies.

Last Modified: 9/10/2014
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