ArticleFrontiers in genetics2022
Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 10 citations in OpenAlex.
- Low-pass whole-genome sequencing reveals genomic diversity and ecotype-specific adaptation in indigenous Tigrayan chickens.Scientific reports · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- Bayesian fine-mapping pinpoints candidate genes and pleiotropic loci of production traits from a chicken backcrossing scheme.BMC genomics · 2026Article
- TEAD4 Promotes Myogenic Differentiation of Porcine Skeletal Muscle Satellite Cells.Animals : an open access journal from MDPI · 2026Article
- Whole-genome sequencing GWAS reveals bovine genomic effects on enteric methane emissions in beef cattle.Scientific reports · 2025Article
- Whole-Genome Sequencing Reveals the Role of Cis-Regulatory Elements and eQTL/sQTL in the Adaptive Selection of Hubei Indigenous Cattle.Animals : an open access journal from MDPI · 2025Article
- Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.BMC genomics · 2025Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Imputed whole-genome sequence (WGS) has been proposed to improve genome-wide association studies (GWAS), since all causative mutations responsible for phenotypic variation are expected to be present in the data. This approach was applied on a large number of purebred (PB) and crossbred (CB) pigs for 18 pork color traits to evaluate the impact of using imputed WGS relative to medium-density marker panels. The traits included Minolta A*, B*, and L* for fat (FCOL), quadriceps femoris muscle (QFCOL), thawed loin muscle (TMCOL), fresh ham gluteus medius (GMCOL), ham iliopsoas muscle (ICOL), and longissimus dorsi muscle on the fresh loin (FMCOL). Sequence variants were imputed from a medium-density marker panel (61K for CBs and 50K for PBs) in all genotyped pigs using BeagleV5.0. We obtained high imputation accuracy (average of 0.97 for PBs and 0.91 for CBs). GWAS were conducted for three datasets: 954 CBs and 891 PBs, and the combined CBs and PBs. For most traits, no significant associations were detected, regardless of panel density or population type. However, quantitative trait loci (QTL) regions were only found for a few traits including TMCOL Minolta A* and GMCOL Minolta B* (CBs), FMCOL Minolta B*, FMCOL Minolta L*, and ICOL Minolta B* (PBs) and FMCOL Minolta A*, FMCOL Minolta B*, GMCOL Minolta B*, and ICOL Minolta B* (Combined dataset). More QTL regions were identified with WGS (
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