ArticleJournal of animal science and biotechnology2023
The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle.
Article in Journal of animal science and biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 55 citations in OpenAlex.
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- Transcriptomic and regulatory landscape of liver tissue associated with meat and carcass quality traits in cattle.Journal of animal science and biotechnology · 2026Article
- Multi-Omics Integration Identifies ABCD4 as a Key Regulator of Backfat Thickness and Lipid Deposition in Pietrain Pigs.Animal genetics · 2026Article
- Integrating bulk and single-cell RNA sequencing with GWAS reveals regulatory networks underpinning complex traits in beef cattle.Journal of animal science and biotechnology · 2026Article
- Activation of the RAS/PPARα pathway reduces backfat deposition of Gayal (Bos frontalis).BMC genomics · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Identification and Characterization of sQTLs and eQTLs Associated with Growth Traits in Yellow-Feathered Broilers.Poultry science · 2026Article
- Insulin-like growth factor 2 as a central regulator of growth and metabolic efficiency in livestock: Genetic, nutritional, and biotechnological perspectives.Veterinary world · 2026Review
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- Integrative analysis of GWAS, Bayesian fine-mapping, Mendelian randomization and colocalization reveals genetic determinants underlying milk-related traits in dairy cattle.Genetics, selection, evolution : GSE · 2026Article
- Multi-omics dissection of the genetic regulation underlying fatty acid composition in cattle.Genome biology · 2025Article
- Review
- Identification of Expression Quantitative Trait Loci (eQTL) for Adipose-Specific Regulatory Mechanisms in Hanwoo (Korean Cattle).Animals : an open access journal from MDPI · 2025Article
- Transforming beef quality through healthy breeding: a strategy to reduce carcinogenic compounds and enhance human health: a review.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Review
- Integrative pigGTEx resource with GWAS reveals genetic mechanism underlying semen quality in boars.Journal of animal science and biotechnology · 2025Article
- Development and Application of a 40 K Liquid Capture Chip for Beef Cattle.Animals : an open access journal from MDPI · 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
- Identification of Gene Expression and Splicing QTLs in Porcine Muscle Associated with Meat Quality Traits.Animals : an open access journal from MDPI · 2025Article
- Identification of Candidate Genes and eQTLs Related to Porcine Reproductive Function.Animals : an open access journal from MDPI · 2025Article
- Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle.Communications biology · 2025Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundA detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit in beef cattle. To prioritize the putative variants and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle. Then, we applied expression quantitative trait loci (eQTL) mapping between the genotype variants and transcriptome of three tissues (longissimus dorsi muscle, backfat, and liver) in 120 cattle.
resultsWe identified 1,580 association signals for 21 beef agronomic traits using GWAS. We then illuminated 854,498 cis-eQTLs for 6,017 genes and 46,970 trans-eQTLs for 1,903 genes in three tissues and built a synergistic network by integrating transcriptomics with agronomic traits. These cis-eQTLs were preferentially close to the transcription start site and enriched in functional regulatory regions. We observed an average of 43.5% improvement in cis-eQTL discovery using multi-tissue eQTL mapping. Fine-mapping analysis revealed that 111, 192, and 194 variants were most likely to be causative to regulate gene expression in backfat, liver, and muscle, respectively. The transcriptome-wide association studies identified 722 genes significantly associated with 11 agronomic traits. Via the colocalization and Mendelian randomization analyses, we found that eQTLs of several genes were associated with the GWAS signals of agronomic traits in three tissues, which included genes, such as NADSYN1, NDUFS3, LTF and KIFC2 in liver, GRAMD1C, TMTC2 and ZNF613 in backfat, as well as TIGAR, NDUFS3 and L3HYPDH in muscle that could serve as the candidate genes for economic traits.
conclusionsThe extensive atlas of GWAS, eQTL, fine-mapping, and transcriptome-wide association studies aid in the suggestion of potentially functional variants and genes in cattle agronomic traits and will be an invaluable source for genomics and breeding in beef cattle.
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