Abstract
BackgroundIt is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information.MethodsThe 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.ResultsWe 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.ConclusionsOur 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.
Highlights
It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and quantitative trait locus (QTL) and on genetic relationships
The objective of this study was to investigate the accuracy of genome-wide breeding values (GW-estimated breeding values (EBV)) prediction using IBS relationships based on linkage disequilibrium (LD) and using genomic IBD relationships based on a limited number of generations within a known pedigree, and how much IBS information can Number of animals improve the accuracy of GW-EBV over and above the use of IBD information
The results show that the accuracy of GW-EBV obtained by IBD relationships, estimated through linkage analysis using four or more generations of pedigree and marker information of the bulls, cannot be improved by including IBS information
Summary
It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL and on genetic relationships. With the availability of genome-wide, dense molecular markers, genomic selection (GS) has become practical and its effectiveness in dairy cattle breeding has been demonstrated in many countries [1,2,3,4,5,6] In this approach, genome-wide breeding values (GW-EBV) are predicted through the. Since mutations occurred on average 2Ne generations ago, where Ne is the effective population size, IBS can consider relationships up to 2Ne generations back in time, while IBD takes into account only generations back to the founders of the known pedigree. The implications of these studies are that GS combines information on LD among founders and relationships between known relatives (IBD relationships)
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