Genomic selection using different marker types and densities.

Journal of Animal Science
T R SolbergT H E Meuwissen

Abstract

With the availability of high-density marker maps and cost-effective genotyping, genomic selection methods may provide faster genetic gain than can be achieved by current selection methods based on phenotypes and the pedigree. Here we investigate some of the factors driving the accuracy of genomic selection, namely marker density and marker type (i.e., microsatellite and SNP markers), and the use of marker haplotypes versus marker genotypes alone. Different densities were tested with marker densities equivalent to 2, 1, 0.5, and 0.25N(e) markers/morgan using microsatellites and 8, 4, 2, and 1N(e) markers/morgan using SNP, where 1N(e) markers/morgan means 100 markers per morgan, if effective size (N(e)) is 100. Marker characteristics and linkage disequilibria were obtained by simulating a population over 1,000 generations to achieve a mutation drift balance. The marker designs were evaluated for their accuracy of predicting breeding values from either estimating marker effects or estimating effects of haplotypes based upon combining 2 markers. Using microsatellites as direct marker effects, the accuracy of selection increased from 0.63 to 0.83 as the density increased from 0.25N(e)/morgan to 2N(e)/morgan. Using SNP markers as di...Continue Reading

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