%0 Journal Article
%T The importance of identity-by-state information for the accuracy of genomic selection
%A Tu Luan
%A John A Woolliams
%A J£¿rgen £¿deg£¿rd
%A Marlies Dolezal
%A Sergio I Roman-Ponce
%A Alessandro Bagnato
%A Theo HE Meuwissen
%J Genetics Selection Evolution
%D 2012
%I BioMed Central
%R 10.1186/1297-9686-44-28
%X The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci). The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data.We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree.Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require pedigree data, it does use the available pedigree structure. Our findings may explain why the prediction equations derived for one breed may not predict accurate genome-wide breeding values when applied to other breeds, since family structures differ among breeds.Substantial advances in genotyping technology have been achieved over the past decade. With the availability of genome-wide, dense molecular markers, genomic selection (GS) has now become practical and its effectiveness in dairy cattle breeding has been demonstrated in many countries [1-6]. In this approach, genome-wide breeding values (GW-EBV) are predicted
%U http://www.gsejournal.org/content/44/1/28