Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed...
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/655 |
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| author | Yachun Han Tao Tan Zixin Li Zheng Ma Ganqiu Lan Jing Liang Kui Li Lijing Bai |
| author_facet | Yachun Han Tao Tan Zixin Li Zheng Ma Ganqiu Lan Jing Liang Kui Li Lijing Bai |
| author_sort | Yachun Han |
| collection | DOAJ |
| description | Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future. |
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| language | English |
| last_indexed | 2024-03-11T06:30:11Z |
| publishDate | 2023-03-01 |
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| series | Genes |
| spelling | doaj.art-913e39ca982048cb98e3d47cd71bce962023-11-17T11:17:35ZengMDPI AGGenes2073-44252023-03-0114365510.3390/genes14030655Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan PigsYachun Han0Tao Tan1Zixin Li2Zheng Ma3Ganqiu Lan4Jing Liang5Kui Li6Lijing Bai7Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaCollege of Animal Science & Technology, Guangxi University, Nanning 530003, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaCollege of Animal Science & Technology, Guangxi University, Nanning 530003, ChinaCollege of Animal Science & Technology, Guangxi University, Nanning 530003, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, ChinaHenan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.https://www.mdpi.com/2073-4425/14/3/655signatures of selectionpig high-density SNP chipQTLannotation |
| spellingShingle | Yachun Han Tao Tan Zixin Li Zheng Ma Ganqiu Lan Jing Liang Kui Li Lijing Bai Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs Genes signatures of selection pig high-density SNP chip QTL annotation |
| title | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
| title_full | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
| title_fullStr | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
| title_full_unstemmed | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
| title_short | Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs |
| title_sort | identification of selection signatures and loci associated with important economic traits in yunan black and huainan pigs |
| topic | signatures of selection pig high-density SNP chip QTL annotation |
| url | https://www.mdpi.com/2073-4425/14/3/655 |
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