Accuracy of Genotype Imputation Using the Geneseek Genomic Profiler for Porcine LD

Genotype imputation of high density genotypes will improve cost efficiency for genomic selection. The newly available GeneSeek Genomic Profiler for Porcine LD (GGP-Porcine) enables accurate imputation of the PorcineSNP60 BeadChip. The objective of this study was to investigate variables affecting imputation accuracy (IA).

High density genotypes (62K) were available for 889 Yorkshire samples. Genotypes and inferred haplotypes were also available for a reference panel of 64 Yorkshire animals genotyped in 32 sire/dam/offspring trios. Imputations were performed using the BEAGLE software. Accuracy was estimated as the proportion of correctly imputed alleles, and the squared correlation between observed and imputed allelic dosages.

Imputation accuracy improved as the number of reference haplotypes increased from 128 (IA=0.955) to 256 (IA=0.971). Accuracy reached a plateau of 0.985 when the reference panel contained 512 haplotypes. Results were consistent across panels assembled from either trios or randomly sampled individuals. Consequently, if no population haplotype reference panel is available, it is more cost effective to randomly sample individuals.

SNP either with low minor allele frequencies or located in the chromosomal extremes had generally slightly below average IA. However, increasing the number of reference haplotypes mitigated this problem.

In conclusion, the GGP-Porcine chip can be used to impute genotypes with high accuracy, even when imputation is based on relatively small panels of reference haplotypes. Average IA can be further increased by adding haplotypes to the reference panel. We expect that the use of imputed genotypes in swine breeding will yield highly accurate predictions of genomic breeding values.