%0 Journal Article
%T Deregressed EBV as the response variable yield more reliable genomic predictions than traditional EBV in pure-bred pigs
%A Tage Ostersen
%A Ole F Christensen
%A Mark Henryon
%A Bjarne Nielsen
%A Guosheng Su
%A Per Madsen
%J Genetics Selection Evolution
%D 2011
%I BioMed Central
%R 10.1186/1297-9686-43-38
%X Reliabilities of genomic breeding values were estimated with EBV and deregressed EBV as response variables and under the three statistical methods, genomic BLUP, Bayesian Lasso and MIXTURE. The methods were examined by splitting data into a reference data set of 1375 genotyped animals that were performance tested before October 2008, and 536 genotyped validation animals that were performance tested after October 2008. The traits examined were daily gain and feed conversion ratio.Using deregressed EBV as the response variable yielded 18 to 39% higher reliabilities of the genomic breeding values than using EBV as the response variable. For daily gain, the increase in reliability due to deregression was significant and approximately 35%, whereas for feed conversion ratio it ranged between 18 and 39% and was significant only when MIXTURE was used. Genomic BLUP, Bayesian Lasso and MIXTURE had similar reliabilities.Deregressed EBV is the preferred response variable, whereas the choice of statistical method is less critical for pure-bred pigs. The increase of 18 to 39% in reliability is worthwhile, since the reliabilities of the genomic breeding values directly affect the returns from genomic selection.Genomic selection in pure-bred pigs can be implemented using a multi-step procedure. Effects of dense genetic markers are estimated using a reference population and these effects are used to predict genomic breeding values (GBV) of selection candidates [1]. Implementing a multi-step procedure relies on two prerequisites: 1) a response variable that summarises the genetic information for reference animals, and 2) a statistical method that associates the response variable to the marker information. The choice of response variable and statistical method may well depend on the data structure. Therefore, the challenge is to find a suitable response variable and statistical method that can handle pure-bred pig data.Pure-bred pig data often have low and varying reliabilities of est
%U http://www.gsejournal.org/content/43/1/38