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 homozygous 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 Single Nucleotide Polymorphisms (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. Samples from 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 85 piglets, respectively. Rate of rejection in true parent–offspring relationships was estimated as 0.000735. This is a lower bound of the genotyping error since rate of rejection depends on allele frequencies. After accounting for allele frequencies, our estimate of the genotyping error is 0.6%. A total of 7,744 SNPs were rejected in five or more true parent–offspring relationships facilitating identification of “problematic” SNPs with inconsistent inheritance in multiple parent–offspring relationships. 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.