First-degree relationships and genotyping errors deciphered by a high-density SNP array in a Duroc × Iberian pig...

Area of Science:

• Animal Genetics
• Genomic Selection
• Bioinformatics

Background:

• First-degree relatives share approximately 50% of alleles.
• Genetic exclusion principle states parent-offspring relationships cannot be homozygous for alternative alleles.

Purpose of the Study:

• To apply genetic exclusion to HD arrays for estimating first-degree relationship rejection rates.
• To estimate parentage and genotyping errors using an Expectation-Maximization algorithm.
• To identify "problematic" Single Nucleotide Polymorphisms (SNPs) with inconsistent inheritance.

Main Methods:

• Utilized the genetic exclusion concept on HD arrays for pigs (Duroc x Iberian).
• Applied an Expectation-Maximization algorithm for parentage estimation and genotyping error assessment.
• Analyzed 214 barrows from nine sires and 55 dams, typed on the HD porcine Affymetrix array.

Main Results:

• Successfully established paternity for 75 piglets and maternity for 85 piglets.
• Estimated the rate of rejection in true parent-offspring relationships at 0.000735.
• Calculated a genotyping error rate of 0.6% after accounting for allele frequencies and identified 7,744 problematic SNPs.

Conclusions:

• Animal experiments and genomic selection genotyping can verify first-degree relationships.
• Genotyping error rates can be estimated for batches of animals or experiments.
• The study demonstrates a reliable method for relationship verification and quality control in genetic data.