Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds
Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We...
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BioMed Central
2015-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-13-137.pdf |
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| author | HyoYoung Kim Kelsey Caetano-Anolles Minseok Seo Young-jun Kwon Seoae Cho Kangseok Seo Heebal Kim |
| author_facet | HyoYoung Kim Kelsey Caetano-Anolles Minseok Seo Young-jun Kwon Seoae Cho Kangseok Seo Heebal Kim |
| author_sort | HyoYoung Kim |
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| description | Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc.These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively. |
| format | Article |
| id | doaj-art-146078780ae9415db54a59d88bf6dc99 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2015-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-146078780ae9415db54a59d88bf6dc992025-02-02T06:10:38ZengBioMed CentralGenomics & Informatics1598-866X2234-07422015-12-0113413714510.5808/GI.2015.13.4.137139Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig BreedsHyoYoung Kim0Kelsey Caetano-Anolles1Minseok Seo2Young-jun Kwon3Seoae Cho4Kangseok Seo5Heebal Kim6Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA.Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea.Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea.C&K Genomics Inc., Seoul National University Research Park, Seoul 08826, Korea.Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Korea.Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5), Landrace (n = 13), and Duroc (n = 6). An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc.These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs) related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718) in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.http://genominfo.org/upload/pdf/gni-13-137.pdfnon-synonymousswinepositive selectionre-sequencingsingle nucleotide polymorphism |
| spellingShingle | HyoYoung Kim Kelsey Caetano-Anolles Minseok Seo Young-jun Kwon Seoae Cho Kangseok Seo Heebal Kim Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds Genomics & Informatics non-synonymous swine positive selection re-sequencing single nucleotide polymorphism |
| title | Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds |
| title_full | Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds |
| title_fullStr | Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds |
| title_full_unstemmed | Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds |
| title_short | Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds |
| title_sort | prediction of genes related to positive selection using whole genome resequencing in three commercial pig breeds |
| topic | non-synonymous swine positive selection re-sequencing single nucleotide polymorphism |
| url | http://genominfo.org/upload/pdf/gni-13-137.pdf |
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