title: Using the unified relationship matrix adjusted by breed-wise allele frequencies in genomic evaluation of a multibreed population.
abstract: The observed low accuracy of genomic selection in multibreed and admixed populations results from insufficient linkage disequilibrium between markers and trait loci. Failure to remove variation due to the population structure may also hamper the prediction accuracy. We verified if accounting for breed origin of alleles in the calculation of genomic relationships would improve the prediction accuracy in an admixed population. Individual breed proportions derived from the pedigree were used to estimate breed-wise allele frequencies (AF). Breed-wise and across-breed AF were estimated from the currently genotyped population and also in the base population. Genomic relationship matrices (G) were subsequently calculated using across-breed (GAB) and breed-wise (GBW) AF estimated in the currently genotyped and also in the base population. Unified relationship matrices were derived by combining different G with pedigree relationships in the evaluation of genomic estimated breeding values (GEBV) for genotyped and ungenotyped animals. The validation reliabilities and inflation of GEBV were assessed by a linear regression of deregressed breeding value (deregressed proofs) on GEBV, weighted by the reliability of deregressed proofs. The regression coefficients (b1) from GAB ranged from 0.76 for milk to 0.90 for protein. Corresponding b1 terms from GBW ranged from 0.72 to 0.88. The validation reliabilities across 4 evaluations with different G were generally 36, 40, and 46% for milk, protein, and fat, respectively. Unexpectedly, validation reliabilities were generally similar across different evaluations, irrespective of AF used to compute G. Thus, although accounting for the population structure in GBW tends to simplify the blending of genomic- and pedigree-based relationships, it appeared to have little effect on the validation reliabilities.
authors.affiliation: Department of Agricultural Sciences PO Box 27 FIN-00014 University of Helsinki, Finland; MTT Agrifood Research Finland, Biotechnology and Food Research, Biometrical Genetics, FIN-31600 Jokioinen, Finland. Electronic address: mahlako.makgahlela@helsinki.fi.
authors.forename: M L
authors.initials: ML
authors.lastname: Makgahlela
authors.affiliation: Department of Agricultural Sciences PO Box 27 FIN-00014 University of Helsinki, Finland; MTT Agrifood Research Finland, Biotechnology and Food Research, Biometrical Genetics, FIN-31600 Jokioinen, Finland.
authors.forename: I
authors.initials: I
authors.lastname: Strandén
authors.affiliation: Danish Agricultural Advisory Service, Udkaersvej 15, 8200 Aarhus, Denmark.
authors.forename: U S
authors.initials: US
authors.lastname: Nielsen
authors.affiliation: Department of Mathematical Sciences, and; Department of Biology and Biocenter Oulu, PO Box 3000 FIN-90014 University of Oulu, Finland.
authors.forename: M J
authors.initials: MJ
authors.lastname: Sillanpää
authors.affiliation: MTT Agrifood Research Finland, Biotechnology and Food Research, Biometrical Genetics, FIN-31600 Jokioinen, Finland.
authors.forename: E A
authors.initials: EA
authors.lastname: Mäntysaari
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D005787:Gene Frequency; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D005838:Genotype; D015810:Linkage Disequilibrium; D008892:Milk; D008957:Models, Genetic; D010375:Pedigree; D010641:Phenotype; D015203:Reproducibility of Results
keywords: adjusted unified relationship matrix; admixed cattle population; allele frequency; genomic estimated breeding value