ArticleNature communications2021
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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Who cites it
129 citing papers in PubMed, 237 citations in OpenAlex.
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Functional genomic dissection and prediction of body size traits in pigs.Genetics, selection, evolution : GSE · 2026Article
- Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.Molecular biology and evolution · 2026Article
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle.Journal of animal science and biotechnology · 2026Article
- Gene co-expression networks related to intramuscular fatty acid composition across different pig genotypes.BMC genomics · 2026Article
- Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics.bioRxiv : the preprint server for biology · 2026Article
- Article
- Multi-omics characterization identifies conserved candidate gene and reveals breed-specific regulatory mechanisms underlying growth-related traits in pigs.BMC genomics · 2026Article
- Porcine MutBERT: a family of lightweight genomic foundation models for functional element prediction in pigs.Briefings in bioinformatics · 2026Article
- Integrative characterization of tissue-specific 3D genome organization and associated transcriptional regulation in pig liver and muscle.Functional & integrative genomics · 2026Article
- Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis.Journal of animal science and biotechnology · 2026Article
- Multi-Omics Epigenetic Landscape Unveils Regulatory Mechanisms Underlying Heterosis in Sheep Muscle Development.Animals : an open access journal from MDPI · 2026Article
- Perinatal brain developmental transition revealed by transcriptomic and proteomic analyses of Bama miniature pigs.Nature communications · 2026Article
- Mendelian randomization and colocalization reveal potential causal effects of average daily gain on carcass composition and reproductive traits in pigs.Journal of animal science and biotechnology · 2026Article
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- Tissue-specific epigenetic regulation of fat metabolism in pigs through integrated analysis of DNA methylation and gene expression networks.Journal of animal science and biotechnology · 2026Article
- Review
- Meta-GWAS of Pig Semen Quality Traits Reveals Conserved Genes Regulating Mammalian Fertility.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Construction of a Multitissue Cell Atlas Reveals Cell-Type-Specific Regulation of Molecular and Complex Phenotypes in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
69 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 8 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases.
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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 Socratic graph.