Discovery of hidden pedigree errors combining genomic information with the Genomic Relationship Matrix in Texel sheep

K Kaseja*, S Mucha, John Yates, Ed Smith, G Banos, JE Conington

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Downloads (Pure)

Abstract

Genomic variants such as Single Nucleotide Polymorphisms and animal pedigree are now used widely in routine genetic evaluations of livestock in many countries. The use of genomic information not only can be used to enhance the accuracy of prediction but also to verify pedigrees for animals that are extensively managed using natural mating and enabling multiple-sire mating groups to be used. By so doing, the rate of genetic gain is enhanced, and any bias associated with incorrect pedigrees is removed. This study used a set of 8 764 sheep genotypes to verify the pedigree based on both the conventional opposing homozygote method as well as a novel method when combined with the inclusion of the genomic relationship matrix (GRM). The genomic relationship coefficients between verified pairs of animals showed on average a relationship of 0.50 with parent, 0.25 with grandparent, 0.13 with great grandparent, 0.50 with full-sibling and 0.27 with half-sibling. Minimum obtained values from these verified pairs were then used as thresholds to determine the pedigree for unverified pairs of animals, to detect potential errors in the pedigree. Using a case study from a population partially genotyped UK sheep, the results from this study illustrate a powerful way to resolve parentage inconsistencies, when combining the conventional ‘opposing homozygote’ method using genomic information together with GRM for pedigree checking. In this way, previously undetected pedigree errors can be resolved.

Original languageEnglish
Article number100468
JournalAnimal
Volume16
Issue number3
Early online date18 Feb 2022
DOIs
Publication statusPrint publication - Mar 2022

Bibliographical note

Publisher Copyright: © 2022 The Authors

Keywords

  • Genotyping
  • pedigree information
  • pedigree verification
  • quality control
  • relationship coefficient
  • Relationship coefficient
  • Pedigree information
  • Quality control
  • Pedigree verification

Fingerprint

Dive into the research topics of 'Discovery of hidden pedigree errors combining genomic information with the Genomic Relationship Matrix in Texel sheep'. Together they form a unique fingerprint.

Cite this