SynthesisPLoS genetics2023
Integrated analysis of genome-wide association studies and 3D epigenomic characteristics reveal the BMP2 gene regulating loin muscle depth in Yorkshire pigs.
Synthesis in PLoS genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
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- Genome-wide identification of the H3K27ac signals reveals key thermogenic cis-regulatory elements of brown adipose tissues in Oryctolagus cuniculus.BMC genomics · 2025Article
- Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States.International journal of molecular sciences · 2025Article
- Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).BMC genomics · 2025Article
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- Genome-Wide Association Study Reveals Novel Loci and Candidate Genes for Birth Weight in Pigs.Animals : an open access journal from MDPI · 2025Article
- Changes in allele frequencies and genetic architecture due to selection in two pig populations.Genetics, selection, evolution : GSE · 2024Article
- Oxidative stress controls lncRNA-mediated sow granulosa cell functions in a FoxO1-dependent manner.Journal of animal science and biotechnology · 2024Article
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- A Mutation Losing an RBP-Binding Site in the LncRNA NORSF Transcript Influences Granulosa Cell Apoptosis and Sow Fertility.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Bone Morphogenetic Protein 2 Enhances Porcine Beige Adipogenesis via AKT/mTOR and MAPK Signaling Pathways.International journal of molecular sciences · 2024Article
- A genome-wide association study identified candidate regions and genes for commercial traits in a Landrace population.Frontiers in genetics · 2024Article
- A Functional Variant Alters the Binding ofAnimals : an open access journal from MDPI · 2023Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe lack of integrated analysis of genome-wide association studies (GWAS) and 3D epigenomics restricts a deep understanding of the genetic mechanisms of meat-related traits. With the application of techniques as ChIP-seq and Hi-C, the annotations of cis-regulatory elements in the pig genome have been established, which offers a new opportunity to elucidate the genetic mechanisms and identify major genetic variants and candidate genes that are significantly associated with important economic traits. Among these traits, loin muscle depth (LMD) is an important one as it impacts the lean meat content. In this study, we integrated cis-regulatory elements and genome-wide association studies (GWAS) to identify candidate genes and genetic variants regulating LMD.
resultsFive single nucleotide polymorphisms (SNPs) located on porcine chromosome 17 were significantly associated with LMD in Yorkshire pigs. A 10 kb quantitative trait locus (QTL) was identified as a candidate functional genomic region through the integration of linkage disequilibrium and linkage analysis (LDLA) and high-throughput chromosome conformation capture (Hi-C) analysis. The BMP2 gene was identified as a candidate gene for LMD based on the integrated results of GWAS, Hi-C meta-analysis, and cis-regulatory element data. The identified QTL region was further verified through target region sequencing. Furthermore, through using dual-luciferase assays and electrophoretic mobility shift assays (EMSA), two SNPs, including SNP rs321846600, located in the enhancer region, and SNP rs1111440035, located in the promoter region, were identified as candidate SNPs that may be functionally related to the LMD.
conclusionsBased on the results of GWAS, Hi-C, and cis-regulatory elements, the BMP2 gene was identified as an important candidate gene regulating variation in LMD. The SNPs rs321846600 and rs1111440035 were identified as candidate SNPs that are functionally related to the LMD of Yorkshire pigs. Our results shed light on the advantages of integrating GWAS with 3D epigenomics in identifying candidate genes for quantitative traits. This study is a pioneering work for the identification of candidate genes and related genetic variants regulating one key production trait (LMD) in pigs by integrating genome-wide association studies and 3D epigenomics.
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