ArticleFrontiers in genetics2014
Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6-week body weight in broiler chickens.
Article in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
114 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits.BMC genomics · 2022Pooled it
- GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle.Scientific reports · 2018Pooled it
- Meta-analysis of genome-wide association from genomic prediction models.Animal genetics · 2016Pooled it
- Weighted Single-Step GWAS Reveals Genetic Mechanisms Underlying Pregnancy Loss in Early Nellore Heifers.Animal genetics · 2026Article
- Genetic Parameters and Genome-Wide Association Studies for Fertility and Reproduction Traits in U.S. Katahdin Sheep Based on the Single-Step GBLUP Methodology.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Weighted Single-Step Genomic Evaluation of Body Structural Traits for Early Selection of Growth Performance in Thai Swamp Buffalo.Animals : an open access journal from MDPI · 2026Article
- Genetic Parameters and Weighted Single-Step Genome-Wide Association Studies of Fertility Traits in Chinese Holstein.Animals : an open access journal from MDPI · 2026Article
- Genomic Prediction and Genome-Wide Association Analysis of Heat Tolerance for Milk Yield in Buffaloes Using a Reaction Norm Model.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- SNPs with High Linkage Disequilibrium Increase the Explained Genetic Variance and the Reliability of Genomic Predictions.Animals : an open access journal from MDPI · 2026Article
- Article
- Genetic architecture of swine inflammation and necrosis syndrome and its genetic correlation with repeated skin damage scores.Journal of animal science · 2026Article
- Weighted Single-Step Genome-Wide Association Study Identifies Candidate Genes for Carcass Traits and Primal Cut Yields in Hanwoo Cattle.Animals : an open access journal from MDPI · 2026Article
- Single-step genome-wide association study of milk somatic cell scores across multi-cattle breeds in Ethiopia.Animal biotechnology · 2025Article
- Genomic predictions for growth and feed efficiency traits in a duck breeding population.BMC genomics · 2025Article
- Integrating Genomic Selection and Genome-Wide Association Study to Enhance Reproductive Traits in Thai Swamp Buffalo.Animals : an open access journal from MDPI · 2025Article
- Variable selection strategies for genomic prediction of growth and carcass related traits in experimental Nellore cattle herds under different selection criteria.Scientific reports · 2025Article
- Genome Selection and Genome-Wide Association Analyses for Litter Size Traits in Large White Pigs.Animals : an open access journal from MDPI · 2025Article
- Pleiotropic Genes Affecting Milk Production, Fertility, and Health in Thai-Holstein Crossbred Dairy Cattle: A GWAS Approach.Animals : an open access journal from MDPI · 2025Article
- Genome-wide association studies of dairy cattle resistance to digital dermatitis recorded at four distinct lactation stages.Scientific reports · 2025Article
- Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows.PloS one · 2025Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively reweighted single-step genomic BLUP procedures (ssGWAS1 and ssGWAS2), a single-marker model (CGWAS), and BayesB. The ssGWAS methods utilize genomic breeding values (GEBVs) based on combined pedigree, genomic and phenotypic information, while CGWAS and BayesB only utilize phenotypes from genotyped animals or pseudo-phenotypes. In this study, ssGWAS was performed by converting GEBVs to SNP marker effects. Unequal variances for markers were incorporated for calculating weights into a new genomic relationship matrix. SNP weights were refined iteratively. The data was body weight at 6 weeks on 274,776 broiler chickens, of which 4553 were genotyped using a 60 k SNP chip. Comparison of genomic regions was based on genetic variances explained by local SNP regions (20 SNPs). After 3 iterations, the noise was greatly reduced for ssGWAS1 and results are similar to that of CGWAS, with 4 out of the top 10 regions in common. In contrast, for BayesB, the plot was dominated by a single region explaining 23.1% of the genetic variance. This same region was found by ssGWAS1 with the same rank, but the amount of genetic variation attributed to the region was only 3%. These findings emphasize the need for caution when comparing and interpreting results from various methods, and highlight that detected associations, and strength of association, strongly depends on methodologies and details of implementations. BayesB appears to overly shrink regions to zero, while overestimating the amount of genetic variation attributed to the remaining SNP effects. The real world is most likely a compromise between methods and remains to be determined.
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