A Snapshot of CNVs in the Pig Genome

Fadista, João; Nygaard, Marianne; Holm, Lars‐Erik; Thomsen, Bo; Berthou, Christian

doi:10.1371/journal.pone.0003916

Cited by 105 publications

(111 citation statements)

References 61 publications

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“…We also compared CNVRs in this study with previous pig CNV studies [24, 25, 35, 36, 39, 41, 42]. After merging the results of recent reports, a total of 849 out of 3,131 CNVRs (27.75%) with the length of 33.02 Mb in our study overlapped with those previously reported (see Table 4).…”

Section: Resultssupporting

confidence: 57%

Global copy number analyses by next generation sequencing provide insight into pig genome variation

Jiang

Wang

et al. 2014

BMC Genomics

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-593) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 57%

Global copy number analyses by next generation sequencing provide insight into pig genome variation

Jiang

Wang

et al. 2014

BMC Genomics

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“…Calibration ΔCt values were derived from the amplification of reference and test primers on a genomic DNA template from the sheep [30][31][32]. The control sample (Gansu Morden sheep breeding population) and no-template control were also amplified with amplification efficiencies above 90% [33,34]. Out of the160 samples …”

Section: Cnvrs Validation By Quantitative Real Time Pcrmentioning

confidence: 99%

Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

Zhang

et al. 2015

Genomics

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The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.

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“…Few CNVs had been uncovered in pigs until recently when a custom tiling oligonucleotide array was used for screening unrelated individuals on the regions of SSC4, 7, 14 and 17 already sequenced and assembled. This screen identified 37 CNV regions [Fadista et al, 2008]. A feasible approach for CNV genotyping similar to the human CNV array should be developed in the future.…”

Section: Sequencing Progressmentioning

confidence: 99%

The Pig Genome Project Has Plenty to Squeal about

Fan¹,

Gorbach²,

Rothschild³

2011

Cytogenet Genome Res

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Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future ‘systems biology’ that integrates and optimizes the information from all research levels can enhance the pig community’s understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed.

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A Snapshot of CNVs in the Pig Genome

Cited by 105 publications

References 61 publications

Global copy number analyses by next generation sequencing provide insight into pig genome variation

Global copy number analyses by next generation sequencing provide insight into pig genome variation

Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

The Pig Genome Project Has Plenty to Squeal about

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