Genomic selection using different marker types and densities

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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 0.25Ne markers/morgan using microsatellites and 8, 4, 2, and 1Ne markers/morgan using SNP, where 1Ne markers/morgan means 100 markers per morgan, if effective size (Ne) 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 0.25Ne/morgan to 2Ne/morgan. Using SNP markers as direct marker effects, the accuracy of selection increased from 0.69 to 0.86 as the density increased from 1Ne/morgan to 8Ne/morgan. The SNP markers required a 2 to 3 times greater density compared with using microsatellites to achieve a similar accuracy. The biases that genomic selection EBV often show are due to the prediction of marker effects instead of QTL effects, and hence, genomic selection EBV may need rescaling for practical use. Using haplotypes resulted in similar or reduced accuracies compared with using direct marker effects. In practical situations, this means that it is advantageous to use direct marker effects, because this avoids the estimation of marker phases with the associated errors. In general, the results showed that the accuracy remained responsive with small bias to increasing marker density at least up to 8Ne SNP/morgan, where the effective population size was 100 and with the genomic model assumed. For a 30-morgan genome and Ne = 100, this implies that about ~24,000 SNP are needed. Copyright © 2008. . Copyright 2008 Journal of Animal Science