ArticleG3 (Bethesda, Md.)2014
Why breeding values estimated using familial data should not be used for genome-wide association studies.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 3 of them syntheses that pooled it.
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Who cites it
25 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle.G3 (Bethesda, Md.) · 2024Pooled it
- Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs.BMC genomics · 2023Pooled it
- Meta-analysis for milk fat and protein percentage using imputed sequence variant genotypes in 94,321 cattle from eight cattle breeds.Genetics, selection, evolution : GSE · 2020Pooled it
- Across-breed analyses of genome-wide association studies for stature and mammary gland morphology in cattle reveal pleiotropic effects of the Friesian POLLED haplotype.Genetics, selection, evolution : GSE · 2026Article
- Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes.BMC genomics · 2022Article
- Mitochondrial DNA Variation Contributes to the Aptitude for Dressage and Show Jumping Ability in the Holstein Horse Breed.Animals : an open access journal from MDPI · 2022Article
- The effect of single-nucleotide polymorphism in the promoter region of bovine alpha-lactalbumin (LALBA) gene on LALBA expression in milk cells and milk traits of cows.Journal of animal science · 2021Article
- Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda.Frontiers in genetics · 2021Article
- Genome-Wide Association Study Identifies New Candidate Markers for Somatic Cells Score in a Local Dairy Sheep.Frontiers in genetics · 2021Article
- Associations between Bovine β-Defensin 4 Genotypes and Production Traits of Polish Holstein-Friesian Dairy Cattle.Animals : an open access journal from MDPI · 2019Article
- Genome wide association study of body weight and feed efficiency traits in a commercial broiler chicken population, a re-visitation.Scientific reports · 2019Article
- Scanning the genomes of parents for imprinted loci acting in their un-genotyped progeny.Scientific reports · 2019Article
- Deciphering of the Genetic Control of Phenology, Yield, and Pellicle Color in Persian Walnut (Frontiers in plant science · 2019Article
- Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso.Archives animal breeding · 2019Article
- Eigen decomposition expedites longitudinal genome-wide association studies for milk production traits in Chinese Holstein.Genetics, selection, evolution : GSE · 2018Article
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- Performance Gains in Genome-Wide Association Studies for Longitudinal Traits via Modeling Time-varied effects.Scientific reports · 2017Article
- Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle.BMC genetics · 2017Article
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4 authors.
Funding
Abstract
In animal breeding, the genetic potential of an animal is summarized as its estimated breeding value, which is derived from its own performance as well as the performance of related individuals. Here, we illustrate why estimated breeding values are not suitable as a phenotype for genome-wide association studies. We simulated human-type and pig-type pedigrees with a range of quantitative trait loci (QTL) effects (0.5-3% of phenotypic variance) and heritabilities (0.3-0.8). We analyzed 1000 replicates of each scenario with four models: (a) a full mixed model including a polygenic effect, (b) a regression analysis using the residual of a mixed model as a trait score (so called GRAMMAR approach), (c) a regression analysis using the estimated breeding value as a trait score, and (d) a regression analysis that uses the raw phenotype as a trait score. We show that using breeding values as a trait score gives very high false-positive rates (up 14% in human pedigrees and >60% in pig pedigrees). Simulations based on a real pedigree show that additional generations of pedigree increase the type I error. Including the family relationship as a random effect provides the greatest power to detect QTL while controlling for type I error at the desired level and providing the most accurate estimates of the QTL effect. Both the use of residuals and the use of breeding values result in deflated estimates of the QTL effect. We derive the contributions of QTL effects to the breeding value and residual and show how this affects the estimates.
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