ArticleGenetics, selection, evolution : GSE2019
Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies.
Article in Genetics, selection, evolution : GSE, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 4 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Integrated genome-wide association studies, meta-analysis, and Bayesian fine mapping reveal novel quantitative trait loci's and functional candidate genes for vulva traits in large white pigs.Journal of animal science · 2025Pooled 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
- GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data.International journal of molecular sciences · 2022Pooled it
- Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans.BMC genomics · 2022Pooled it
- Imputed whole genome sequence based association pinpoints genetic architecture of labour dystocia of pigs using multi-breed populations.Genetics, selection, evolution : GSE · 2026Article
- Article
- Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds.BMC genomics · 2025Article
- Genomic analyses of withers height and linear conformation traits in German Warmblood horses using imputed sequence-level genotypes.Genetics, selection, evolution : GSE · 2024Article
- Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken.Poultry science · 2024Article
- Genomic regions, candidate genes, and pleiotropic variants associated with physiological and anatomical indicators of heat stress response in lactating sows.BMC genomics · 2024Article
- Genome-wide association and functional genomic analyses for body conformation traits in North American Holstein cattle.Frontiers in genetics · 2024Article
- Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.Genetics, selection, evolution : GSE · 2023Article
- The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs.Communications biology · 2023Article
- The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle.Genetics, selection, evolution : GSE · 2023Article
- GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance toGenes · 2022Article
- Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.Advanced genetics (Hoboken, N.J.) · 2022Article
- Development and validation of a horse reference panel for genotype imputation.Genetics, selection, evolution : GSE · 2022Article
- Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data.Evolutionary applications · 2022Article
- Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats.Animals : an open access journal from MDPI · 2022Article
- Comparison of the choice of animals for re-sequencing in two maternal pig lines.Genetics, selection, evolution : GSE · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundUse of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for the target population. The objective of this study was to investigate imputation to WGS in two pig lines using a multi-line reference population and, subsequently, to investigate the effect of using these imputed WGS (iWGS) for GWAS.
methodsPhenotypes and genotypes were available on 12,184 Large White pigs (LW-line) and 4943 Dutch Landrace pigs (DL-line). Imputed 660 K and 80 K genotypes for the LW-line and DL-line, respectively, were imputed to iWGS using Beagle v.4.1. Since only 32 LW-line and 12 DL-line boars were sequenced, 142 animals from eight commercial lines were added. GWAS were performed for each line using the 80 K and 660 K SNPs, the genotype scores of iWGS SNPs that had an imputation accuracy (Beagle R
resultsFor the DL-line (LW-line), imputation of 80 K genotypes to iWGS resulted in an average Beagle R
conclusionsImputation to WGS using the multi-line reference population resulted in relatively poor imputation, especially when imputing from 80 K (DL-line). In spite of the poor imputation accuracies, using iWGS instead of a lower density SNP chip increased the number of detected QTL and the estimated proportion of phenotypic variance explained by these QTL, especially when dosage scores were used instead of genotype scores. Thus, iWGS, even with poor imputation accuracy, can be used to identify possible interesting regions for fine mapping.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.