importance of identity-by-state information for the accuracy of genomic selection

• Published in: Genetics selection evolution (Paris) Vol. 44; no. 1; p. 28
• Main Authors: Luan, Tu, Woolliams, John A, Ødegård, Jørgen, Dolezal, Marlies, Roman-Ponce, Sergio I, Bagnato, Alessandro, Meuwissen, Theo HE
• Format: Journal Article
• Language: English; German
• Published: France Springer-Verlag 31.08.2012; BioMed Central Ltd; BioMed Central; BMC
• Subjects: Accuracy; Analysis; Animals; Breeding; Brown Swiss; bulls; Cattle - genetics; Data processing; equations; Genetic relationship; Genetics; Genome - genetics; Genomes; Genomics; genotype; Genotypes; Life sciences; Linkage analysis; Linkage Disequilibrium; loci; Male; marker-assisted selection; Markers; Mathematical models; Milk; Models, Genetic; Models, Statistical; Mutation; Pedigree; Polymorphism, Single Nucleotide; Population - genetics; prediction; Predictions; Probability; Quantitative genetics; Quantitative trait loci; Quantitative Trait Loci - genetics; Selection, Genetic; Single-nucleotide polymorphism; Studies; Values
• ISSN: 1297-9686; 0999-193X; 1297-9686
• DOI: 10.1186/1297-9686-44-28

BACKGROUND: 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 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.