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Strategies to Implement Genomic Selection in Pig Breeding using Very Low Marker Density
To reduce the costs of genomic selection, selection candidates can be genotyped with an SNP panel of reduced density. Two strategies for the selection of SNPs to be considered in a very low density SNP panel (384 SNPs) are investigated using 895 progeny tested and genotyped German Piétrain boars. In the first strategy equal spaced SNPs were selected, which were used to impute the high density genotypes. In the second strategy SNPs were selected based on results of association analysis. Accuracies of DGV for the two strategies were obtained from cross validation. A regression approach to correct for the upward bias of the cross validation accuracy of the DGV was used. The first strategy resulted in more accurate DGV. This implies that imputation is beneficial even if only 384 SNPs are genotyped for the selection candidates.
Keywords:
Piétrain sire line
Unbiased DGV accuracies
Very low-density SNP panel
