ArticleBMC genomics2014
Global copy number analyses by next generation sequencing provide insight into pig genome variation.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Genome-wide identification of copy number variations in wrinkled skin cases of Xiang pigs.Scientific reports · 2024Article
- Genome-wide detection of multiple variants associated with teat number in French Yorkshire pigs.BMC genomics · 2024Article
- An effect of large-scale deletions and duplications on transcript expression.Functional & integrative genomics · 2022Article
- Genome-Wide Detection of Structural Variations Reveals New Regions Associated with Domestication in Small Ruminants.Genome biology and evolution · 2021Article
- Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population.Frontiers in genetics · 2021Article
- Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing.BMC genomics · 2020Article
- CNV analysis of Meishan pig by next-generation sequencing and effects ofJournal of animal science and biotechnology · 2020Article
- Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak.Animals : an open access journal from MDPI · 2019Article
- Article
- Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ).Functional & integrative genomics · 2019Article
- A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive.BMC genomics · 2019Article
- Detection of genome-wide structural variations in the Shanghai Holstein cattle population using next-generation sequencing.Asian-Australasian journal of animal sciences · 2019Article
- A global analysis of CNVs in diverse yak populations using whole-genome resequencing.BMC genomics · 2019Article
- A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.Frontiers in genetics · 2019Article
- Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing.BMC genomics · 2017Article
- Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals.BMC genomics · 2017Article
- CNV discovery for milk composition traits in dairy cattle using whole genome resequencing.BMC genomics · 2017Article
- Article
- Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.BMC genomics · 2016Article
- Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare.Genetics, selection, evolution : GSE · 2016Review
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Authors and funding
11 authors.
Funding
Abstract
backgroundCopy number variations (CNVs) confer significant effects on genetic innovation and phenotypic variation. Previous CNV studies in swine seldom focused on in-depth characterization of global CNVs.
resultsUsing whole-genome assembly comparison (WGAC) and whole-genome shotgun sequence detection (WSSD) approaches by next generation sequencing (NGS), we probed formation signatures of both segmental duplications (SDs) and individualized CNVs in an integrated fashion, building the finest resolution CNV and SD maps of pigs so far. We obtained copy number estimates of all protein-coding genes with copy number variation carried by individuals, and further confirmed two genes with high copy numbers in Meishan pigs through an enlarged population. We determined genome-wide CNV hotspots, which were significantly enriched in SD regions, suggesting evolution of CNV hotspots may be affected by ancestral SDs. Through systematically enrichment analyses based on simulations and bioinformatics analyses, we revealed CNV-related genes undergo a different selective constraint from those CNV-unrelated regions, and CNVs may be associated with or affect pig health and production performance under recent selection.
conclusionsOur studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genome variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.
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