ArticleBMC genomics2013
Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep.BMC genomics · 2026Article
- Collagen-Heparin-FGF2-VEGF Scaffolds Induce a Regenerative Gene Expression Profile in a Fetal Sheep Wound Model.Tissue engineering and regenerative medicine · 2024Article
- Genome-Wide Scan for Copy Number Variations in Chinese Merino Sheep Based on Ovine High-Density 600K SNP Arrays.Animals : an open access journal from MDPI · 2024Article
- Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle.International journal of molecular sciences · 2024Article
- Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle.BMC genomics · 2024Article
- Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits.Frontiers in veterinary science · 2023Review
- Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds.Scientific reports · 2022Article
- Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds.Scientific reports · 2022Article
- Breeding of African sheep reared under low-input/output smallholder production systems for trypanotolerance.Veterinary world · 2022Review
- Towards the detection of copy number variation from single sperm sequencing in cattle.BMC genomics · 2022Article
- Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds.Animals : an open access journal from MDPI · 2022Article
- Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing.Frontiers in genetics · 2022Article
- Two Different Copy Number Variations of theAnimals : an open access journal from MDPI · 2021Article
- A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing.BMC genomics · 2021Article
- Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population.Frontiers in genetics · 2021Article
- Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep.Frontiers in genetics · 2021Article
- Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations.Animals : an open access journal from MDPI · 2020Article
- Copy Number Variation of theAnimals : an open access journal from MDPI · 2020Article
- Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays.Frontiers in genetics · 2020Article
- Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits.Frontiers in genetics · 2020Article
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11 authors.
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Abstract
backgroundIn recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.
resultsAnalyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.
conclusionsIn this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.
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