RESUMO
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.
