Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs
Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild...
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MDPI AG
2022-11-01
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| author | Wei Zhang Mei Zhou Linqing Liu Shiguang Su Lin Dong Xinxin Meng Xueting Li Chonglong Wang |
| author_facet | Wei Zhang Mei Zhou Linqing Liu Shiguang Su Lin Dong Xinxin Meng Xueting Li Chonglong Wang |
| author_sort | Wei Zhang |
| collection | DOAJ |
| description | Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (<i>NDN</i>, <i>TMOD4</i>, <i>SFRP1</i>, and <i>SMYD3</i>), reproduction related (<i>GJA1</i>, <i>CYP26B1</i>, <i>WNT5A</i>, <i>SRD5A2</i>, <i>PTPN11</i>, <i>SPEF2</i>, and <i>CCNB1</i>), residual feed intake (RFI) related (<i>MAP3K5</i>), and ear size related (<i>WIF1</i>). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig. |
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| last_indexed | 2024-03-09T19:03:29Z |
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| spelling | doaj.art-61689b5b891a4c17986bc7daee67350f2023-11-24T04:48:37ZengMDPI AGGenes2073-44252022-11-011311202610.3390/genes13112026Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous PigsWei Zhang0Mei Zhou1Linqing Liu2Shiguang Su3Lin Dong4Xinxin Meng5Xueting Li6Chonglong Wang7Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaKey Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, ChinaSingle nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (<i>NDN</i>, <i>TMOD4</i>, <i>SFRP1</i>, and <i>SMYD3</i>), reproduction related (<i>GJA1</i>, <i>CYP26B1</i>, <i>WNT5A</i>, <i>SRD5A2</i>, <i>PTPN11</i>, <i>SPEF2</i>, and <i>CCNB1</i>), residual feed intake (RFI) related (<i>MAP3K5</i>), and ear size related (<i>WIF1</i>). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.https://www.mdpi.com/2073-4425/13/11/2026Wannan black pigAsian wild boarcopy number variation (CNV)selection signaturesfixation index (F<sub>ST</sub>)whole genome resequencing |
| spellingShingle | Wei Zhang Mei Zhou Linqing Liu Shiguang Su Lin Dong Xinxin Meng Xueting Li Chonglong Wang Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs Genes Wannan black pig Asian wild boar copy number variation (CNV) selection signatures fixation index (F<sub>ST</sub>) whole genome resequencing |
| title | Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs |
| title_full | Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs |
| title_fullStr | Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs |
| title_full_unstemmed | Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs |
| title_short | Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs |
| title_sort | population structure and selection signatures underlying domestication inferred from genome wide copy number variations in chinese indigenous pigs |
| topic | Wannan black pig Asian wild boar copy number variation (CNV) selection signatures fixation index (F<sub>ST</sub>) whole genome resequencing |
| url | https://www.mdpi.com/2073-4425/13/11/2026 |
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