Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication
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Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native and domesticated pigs provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection. Here we used whole-genome sequencing to explore the genetic relationships among the European native pig Berkshire and breeds that are distributed worldwide, and to identify genomic footprints left by selection during the domestication of Berkshire. Numerous nonsynonymous SNPs-containing genes fall into olfactory-related categories, which are part of a rapidly evolving superfamily in the mammalian genome. Phylogenetic analyses revealed a deep phylogenetic split between European and Asian pigs rather than between domestic and wild pigs. Admixture analysis exhibited higher portion of Chinese genetic material for the Berkshire pigs, which is consistent with the historical record regarding its origin. Selective sweep analyses revealed strong signatures of selection affecting genomic regions that harbor genes underlying economic traits such as disease resistance, pork yield, fertility, tameness and body length. These discoveries confirmed the history of origin of Berkshire pig by genome-wide analysis and illustrate how domestication has shaped the patterns of genetic variation.
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An analysis of a domesticated pig genome suggests that the involvement of the ERK pathway in domestication extends beyond the species focused on in this study.
“an analysis of a domesticated pig (Sus scrofa domesticus) genome [88] suggests that the involvement of ERK pathway in domestication extends beyond the species we focused on in this study.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [88]
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Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing
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Screening for signatures of selection of Tianzhu white yak using genome‐wide re‐sequencing
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Integrated Analysis of Methylome, Transcriptome and miRNAome of Three Pig Breeds
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Genomic and Phenotypic Divergence in Wild Barley Driven by Microgeographic Adaptation
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Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina
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Deletion in KRT75L4 linked to frizzle feather in Xiushui Yellow Chickens
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Genome‐wide analysis suggests multiple domestication events of Chinese local pigs
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Comprehensive inbred variation discovery in Bama pigs using de novo assemblies
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Self-citationBackcrossing to different parents produced two distinct hybrid species
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Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine
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Genome-wide analysis reveals selection for Chinese Rongchang pigs
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Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution
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Current Status of Cattle Genome Sequencing and Analysis using Next Generation Sequencing
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Phylogeography of feral Monteiro pig in the Brazilian Pantanal Ecosystem
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Positive selection on rare variants of IGF1R and BRD4 underlying the cold adaptation of wild boar
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The role of G protein‐coupled receptors and their ligands in animal domestication
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Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum
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ПОИСК «ОТПЕЧАТКОВ ОТБОРА» У ДОМАШНИХ СВИНЕЙ И ДИКОГО КАБАНА (обзор)
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Pervasive selection pressure in wild and domestic pigsPreprint
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Allele-specific Effects of Three-dimensional Genome Architecture in Hybrid PigsPreprint
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Using genomewide polymorphisms to explore demography and feralization in the pig species
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IDENTIFICATION OF «SELECTION SIGNATURES» IN PIGS AND WILD BOARS (review)
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Genome-Wide Analysis Reveals Genetic Structure and Selective Sweeps in Chinese Indigenous Pig BreedsPreprint
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- Authors
- Li, M., Tian, S., Yeung, C. K. L., Meng, X., Tang, Q., Niu, L., Wang, X., Jin, L., Ma, J., Long, K., Zhou, C., Cao, Y., Zhu, L., Bai, L., Tang, G., Gu, Y., Jiang, A., Li, X., & Li, R.
- Affiliations
- Peking University (CN)
- Novogene Bioinformatics Institute (CN)
- Sichuan Agricultural University (CN)
- Southwest University (CN)
- Sichuan Animal Science Academy (CN)
- Corresponding author
- Li, Mingzhou
- Li, Xuewei
- Li, Ruiqiang
- ORCID
- Venue
- Scientific Reports
- Published
- 2014-04-14
- Volume
- 4
- Issue
- 1
- Pages
- 4678-4678
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC3985078
- OpenAlex
- W2092095322
- Cited by
- 87
- References
- 56
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 3 · 2023: 3 · 2022: 8 · 2021: 10 · 2020: 13 · 2019: 10 · 2018: 7 · 2017: 9 · 2016: 9 · 2015: 10 · 2014: 3
- FWCI
- 6.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Scientific Reports (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- China Postdoctoral Science Foundation
- Science and Technology Facilities Council (ST/J001465/1)
- National High-tech Research and Development Program (2013AA102502)
- Science Fund for Distinguished Young Scholars of Sichuan Province
- Program for Changjiang Scholars and Innovative Research Team in University (IRT13083)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Berkshire pigs, pig domestication, selective sweeps, olfactory genes, non-synonymous SNPs, admixture, disease resistance genes, genetic variation
- MeSH terms
- Animals, Animals, Domestic, Chromosome Mapping, Phylogeny, Selection, Genetic, Swine, Genome, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Body Size, INDEL Mutation, High-Throughput Nucleotide Sequencing
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