ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Development of a whole-exome sequencing kit to facilitate porcine biomedical research.Genome biology · 2025Article
- Genetic Diversity and Population Structure ofAnimals : an open access journal from MDPI · 2025Article
- Discovery of two tightly linked soybean genes at the qSCN10 (O) locus conferring broad-spectrum resistance to soybean cyst nematode.Communications biology · 2025Article
- Influence of MHC on genetic diversity and testicular expression of linked olfactory receptor genes.BMC genomics · 2025Article
- Integrating Genomics and Transcriptomics to Identify Candidate Genes for Egg Production in Taihe Black-Bone Silky Fowls (International journal of molecular sciences · 2024Article
- mRNA expression profiles in muscle-derived extracellular vesicles of Large White and wild boar piglets reveal their potential roles in immunity and muscle phenotype.Frontiers in veterinary science · 2024Article
- Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree.Genomics, proteomics & bioinformatics · 2022Article
- Rare and population-specific functional variation across pig lines.Genetics, selection, evolution : GSE · 2022Article
- Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses.Animals : an open access journal from MDPI · 2022Article
- Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds.Frontiers in genetics · 2022Article
- Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese.Frontiers in veterinary science · 2022Article
- Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes.Genetics, selection, evolution : GSE · 2021Article
- A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism.PLoS genetics · 2020Article
- Molecular and Cellular Mechanisms for PRRSV Pathogenesis and Host Response to Infection.Virus research · 2020Review
- Identification and validation of a novel candidate gene regulating net meat weight in Simmental beef cattle based on imputed next-generation sequencing.Cell proliferation · 2020Article
- Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms.Molecules and cells · 2020Article
- Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds.Journal of animal science · 2020Article
- Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip.Animals : an open access journal from MDPI · 2020Article
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Authors and funding
16 authors.
Funding
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Abstract
Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.
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