A genome-wide detection of copy number variations using SNP genotyping arrays in swine
<p>Abstract</p> <p>Background</p> <p>Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation complementary to single nucleoti...
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BMC
2012-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/273 |
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| author | Wang Jiying Jiang Jicai Fu Weixuan Jiang Li Ding Xiangdong Liu Jian-Feng Zhang Qin |
| author_facet | Wang Jiying Jiang Jicai Fu Weixuan Jiang Li Ding Xiangdong Liu Jian-Feng Zhang Qin |
| author_sort | Wang Jiying |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation complementary to single nucleotide polymorphism (SNP). Comprehensive identification and cataloging of pig CNVs would be of benefit to the functional analyses of genome variation.</p> <p>Results</p> <p>In this study, we performed a genome-wide CNV detection based on the Porcine SNP60 genotyping data of 474 pigs from three pure breed populations (Yorkshire, Landrace and Songliao Black) and one Duroc × Erhualian crossbred population. A total of 382 CNV regions (CNVRs) across genome were identified, which cover 95.76Mb of the pig genome and correspond to 4.23% of the autosomal genome sequence. The length of these CNVRs ranged from 5.03 to 2,702.7kb with an average of 250.7kb, and the frequencies of them varied from 0.42 to 20.87%. These CNVRs contains 1468 annotated genes, which possess a great variety of molecular functions, making them a promising resource for exploring the genetic basis of phenotypic variation within and among breeds. To confirmation of these findings, 18 CNVRs representing different predicted status and frequencies were chosen for validation via quantitative real time PCR (qPCR). Accordingly, 12 (66.67%) of them was successfully confirmed.</p> <p>Conclusions</p> <p>Our results demonstrated that currently available Porcine SNP60 BeadChip can be used to capture CNVs efficiently. Our study firstly provides a comprehensive map of copy number variation in the pig genome, which would be of help for understanding the pig genome and provide preliminary foundation for investigating the association between various phenotypes and CNVs.</p> |
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| language | English |
| last_indexed | 2024-12-14T04:52:36Z |
| publishDate | 2012-06-01 |
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| spelling | doaj.art-6495f99b65ad4d5b9a418c9d3cc6bde42022-12-21T23:16:30ZengBMCBMC Genomics1471-21642012-06-0113127310.1186/1471-2164-13-273A genome-wide detection of copy number variations using SNP genotyping arrays in swineWang JiyingJiang JicaiFu WeixuanJiang LiDing XiangdongLiu Jian-FengZhang Qin<p>Abstract</p> <p>Background</p> <p>Copy Number Variations (CNVs) have been shown important in both normal phenotypic variability and disease susceptibility, and are increasingly accepted as another important source of genetic variation complementary to single nucleotide polymorphism (SNP). Comprehensive identification and cataloging of pig CNVs would be of benefit to the functional analyses of genome variation.</p> <p>Results</p> <p>In this study, we performed a genome-wide CNV detection based on the Porcine SNP60 genotyping data of 474 pigs from three pure breed populations (Yorkshire, Landrace and Songliao Black) and one Duroc × Erhualian crossbred population. A total of 382 CNV regions (CNVRs) across genome were identified, which cover 95.76Mb of the pig genome and correspond to 4.23% of the autosomal genome sequence. The length of these CNVRs ranged from 5.03 to 2,702.7kb with an average of 250.7kb, and the frequencies of them varied from 0.42 to 20.87%. These CNVRs contains 1468 annotated genes, which possess a great variety of molecular functions, making them a promising resource for exploring the genetic basis of phenotypic variation within and among breeds. To confirmation of these findings, 18 CNVRs representing different predicted status and frequencies were chosen for validation via quantitative real time PCR (qPCR). Accordingly, 12 (66.67%) of them was successfully confirmed.</p> <p>Conclusions</p> <p>Our results demonstrated that currently available Porcine SNP60 BeadChip can be used to capture CNVs efficiently. Our study firstly provides a comprehensive map of copy number variation in the pig genome, which would be of help for understanding the pig genome and provide preliminary foundation for investigating the association between various phenotypes and CNVs.</p>http://www.biomedcentral.com/1471-2164/13/273Copy number variationsGenetic variationSNP arraysQuantitative real time PCRPig |
| spellingShingle | Wang Jiying Jiang Jicai Fu Weixuan Jiang Li Ding Xiangdong Liu Jian-Feng Zhang Qin A genome-wide detection of copy number variations using SNP genotyping arrays in swine BMC Genomics Copy number variations Genetic variation SNP arrays Quantitative real time PCR Pig |
| title | A genome-wide detection of copy number variations using SNP genotyping arrays in swine |
| title_full | A genome-wide detection of copy number variations using SNP genotyping arrays in swine |
| title_fullStr | A genome-wide detection of copy number variations using SNP genotyping arrays in swine |
| title_full_unstemmed | A genome-wide detection of copy number variations using SNP genotyping arrays in swine |
| title_short | A genome-wide detection of copy number variations using SNP genotyping arrays in swine |
| title_sort | genome wide detection of copy number variations using snp genotyping arrays in swine |
| topic | Copy number variations Genetic variation SNP arrays Quantitative real time PCR Pig |
| url | http://www.biomedcentral.com/1471-2164/13/273 |
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