First-Degree Relationships and Genotyping Errors Deciphered by a High-Density SNP Array in a Duroc × Iberian Pig Cross

Abstract Background Two individuals with a first-degree relationship share about 50 percent of their alleles. Parent-offspring relationships cannot be homozygotes for alternative alleles (genetic exclusion). Methods Applying the concept of genetic exclusion to HD arrays typed in animals for experimental purposes or genomic selection allows estimation of the rate of rejection of first-degree relationships as the rate at which two individuals typed for a large number of SNPs do not share at least one allele. An Expectation–Maximization algorithm is applied to estimate parentage. In addition, genotyping errors are estimated in true parent-offspring relationships due to the large number of SNPs. Nine candidate Duroc sires and 55 Iberian dams producing 214 Duroc × Iberian barrows were typed for the HD porcine Affymetrix array. Results We were able to establish paternity and maternity of 75 and 86 piglets, respectively. A lower bound of the genotyping error of 0.003345 was estimated based on the rate of rejection of true parent-offspring relationships among autosomal SNPs. The true genotyping error is estimated to be between twice and three times the average of the rate of rejection observed in true relationships, i.e., between approximately 0.0067 and 0.0100. A total of 8,558 SNPs were rejected in six or more true parent-offspring relationships facilitating identification of “problematic” SNPs with inconsistent inheritance. Conclusions This study shows that animal experiments and routine genotyping in genomic selection allow to establish or to verify first-degree relationships as well as to estimate genotyping errors for each batch of animals or experiment.