Evaluation of the utility of diagonal elements of the genomic relationship matrix as a diagnostic tool to detect mislabelled genotyped animals in a broiler chicken population

• Published in: Journal of animal breeding and genetics (1986) 2011-10, Vol.128 (5), p.386-393
• Main Authors: Simeone, R, Misztal, I, Aguilar, I, Legarra, A
• Format: Article
• Language: English
• Subjects: Allele frequency; alleles; Animal breeding; Animal Husbandry - methods; Animal populations; Animals; Body weight; broiler chickens; chicken; Chickens - genetics; Computer Simulation; data collection; Gene Frequency; genomic relationship matrix; Genomics; Genotype; Genotype & phenotype; loci; Matrix; Models, Genetic; Pedigree; Population genetics; Population studies; Poultry; Reproducibility of Results; Single-nucleotide polymorphism; SNP; Vocalization behavior
• ISSN: 0931-2668; 1439-0388
• DOI: 10.1111/j.1439-0388.2011.00926.x

This study explored distributions of diagonal elements of genomic relationship matrix (G), evaluated the utility of G as a diagnostic tool to detect mislabelled animals in a genomic dataset and evaluated the effect of mislabelled animals on the accuracy of genomic evaluation. Populations of 10 000 animals were simulated with 60 000 SNP varying in allele frequency at each locus between 0.02 and 0.98. Diagonal elements of G were distributed with a single peak (mean = 1.00 ± 0.03) and ranged from 0.84 through 1.36. Mixed populations were also simulated: 7 000 animals with frequencies of second alleles ranging from 0.02 through 0.98 were combined with 1750 or 7000 animals with frequencies of second alleles ranging from 0.0 through 1.0. The resulting distributions of diagonal elements of G were bimodal. Body weight at 6 weeks was provided by Cobb‐Vantress for broiler chickens, of which 3285 were genotyped for 57 636 SNP. Analysis used a combined genomic and pedigree relationship matrix; G was scaled using current allele frequencies. The distribution of diagonal elements was multimodal and ranged from 0.54 to 3.23. Animals with diagonal elements >1.5 were identified as coming from another chicken line or as having low call rates. Removal of mislabelled animals increased accuracy by 0.01. For the studied type of population, diagonal elements of G may be a useful tool to help identify mislabelled animals or secondary populations.