ArticleGenetics, selection, evolution : GSE2020
Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits.
Article in Genetics, selection, evolution : GSE, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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28 citing papers in PubMed, 1 synthesis or guideline pooled it, 70 citations in OpenAlex.
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- Multi-omics dissection of the genetic regulation underlying fatty acid composition in cattle.Genome biology · 2025Article
- Integrative analysis of genome and transcriptome reveals a novel regulator for pork intramuscular fat content.Genetics, selection, evolution : GSE · 2025Article
- Exploring transcriptomic and genomic differences between susceptible and resistant fetal pigs to maternal PRRSV infection at late gestation.Veterinary research · 2025Article
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- A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.BMC biology · 2025Article
- Identification of Gene Expression and Splicing QTLs in Porcine Muscle Associated with Meat Quality Traits.Animals : an open access journal from MDPI · 2025Article
- Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq.BMC genomics · 2025Article
- Comparative Transcriptomic Analysis Provides Insight into Spatiotemporal Expression Patterns of Pivotal Genes During Critical Growth Stages in Min Pig Breed.Biomolecules · 2025Article
- A comprehensive analysis of allele-specific expression and transcriptomic profiling in pig limbic and endocrine tissues.Frontiers in molecular neuroscience · 2025Article
- Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds.Animals : an open access journal from MDPI · 2024Article
- Article
- Comparative transcriptome analysis of longissimus dorsi muscle reveal potential genes affecting meat trait in Chinese indigenous Xiang pig.Scientific reports · 2024Article
- Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle.Genome research · 2024Article
- Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.BMC genomics · 2024Article
- Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs.Frontiers in genetics · 2024Article
- A compendium of genetic regulatory effects across pig tissues.Nature genetics · 2024Article
- Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues.GigaScience · 2022Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundGenetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits.
resultsUsing a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3).
conclusionsThe present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.
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