Increased accuracy of artificial selection by using the realized relationship matrix. (vol 91, pg 47, 2009)

摘要

Dense marker genotypes allow the construction of the realized relationship matrix betweenindividuals, with elements the realized proportion of the genome that is identical by descent (IBD)between pairs of individuals. In this paper, we demonstrate that by replacing the averagerelationship matrix derived from pedigree with the realized relationship matrix in best linearunbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can besubstantially increased, especially for individuals with no phenotype of their own. We furtherdemonstrate that this method of predicting breeding values is exactly equivalent to the genomicselection methodology where the effects of quantitative trait loci (QTLs) contributing to variation inthe trait are assumed to be normally distributed. The accuracy of breeding values predicted using therealized relationship matrix in the BLUP equations can be deterministically predicted for knownfamily relationships, for example half sibs. The deterministic method uses the effective number ofindependently segregating loci controlling the phenotype that depends on the type of familyrelationship and the length of the genome. The accuracy of predicted breeding values depends onthis number of effective loci, the family relationship and the number of phenotypic records. Thedeterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family weregenotyped and phenotyped, and the heritability of the trait was 0.5, the reliability of predictedgenomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was0.82. These results were verified by simulation. A deterministic prediction was also derived forrandom mating populations, where the effective population size is the key parameter determining theeffective number of independently segregating loci. If the effective population size is large, a verylarge number of individuals must be genotyped and phenotyped in order to accurately predictbreeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0.3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes arerequired in order to predict GEBVs of un-phenotyped individuals in the same population with anaccuracy of 0.7.