Genome-wide detection of selective signatures in a Duroc pig population
The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population (n=715) was genoty...
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| Format: | Article |
| Language: | English |
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Elsevier
2018-11-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311918619847 |
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| author | Shu-qi DIAO Yuan-yu LUO Yun-long MA Xi DENG Ying-ting HE Ning GAO Hao ZHANG Jia-qi LI Zan-mou CHEN Zhe ZHANG |
| author_facet | Shu-qi DIAO Yuan-yu LUO Yun-long MA Xi DENG Ying-ting HE Ning GAO Hao ZHANG Jia-qi LI Zan-mou CHEN Zhe ZHANG |
| author_sort | Shu-qi DIAO |
| collection | DOAJ |
| description | The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip. The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure. In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness. Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1. These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes. This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs. |
| first_indexed | 2024-12-19T18:08:39Z |
| format | Article |
| id | doaj.art-91cd1460d2d743fd9a3faeb4884f27e4 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-19T18:08:39Z |
| publishDate | 2018-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-91cd1460d2d743fd9a3faeb4884f27e42022-12-21T20:11:23ZengElsevierJournal of Integrative Agriculture2095-31192018-11-01171125282535Genome-wide detection of selective signatures in a Duroc pig populationShu-qi DIAO0Yuan-yu LUO1Yun-long MA2Xi DENG3Ying-ting HE4Ning GAO5Hao ZHANG6Jia-qi LI7Zan-mou CHEN8Zhe ZHANG9Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.China; DIAO Shu-qiGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.China; Liupanshui Academy of Agricultural Sciences, Liupanshui 553001, P.R.ChinaKey Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Ministry of Education/College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.China; Correspondence CHEN Zan-mouGuangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R.ChinaThe Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip. The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure. In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness. Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1. These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes. This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.http://www.sciencedirect.com/science/article/pii/S2095311918619847Durocselective signaturecandidate genesREHH |
| spellingShingle | Shu-qi DIAO Yuan-yu LUO Yun-long MA Xi DENG Ying-ting HE Ning GAO Hao ZHANG Jia-qi LI Zan-mou CHEN Zhe ZHANG Genome-wide detection of selective signatures in a Duroc pig population Journal of Integrative Agriculture Duroc selective signature candidate genes REHH |
| title | Genome-wide detection of selective signatures in a Duroc pig population |
| title_full | Genome-wide detection of selective signatures in a Duroc pig population |
| title_fullStr | Genome-wide detection of selective signatures in a Duroc pig population |
| title_full_unstemmed | Genome-wide detection of selective signatures in a Duroc pig population |
| title_short | Genome-wide detection of selective signatures in a Duroc pig population |
| title_sort | genome wide detection of selective signatures in a duroc pig population |
| topic | Duroc selective signature candidate genes REHH |
| url | http://www.sciencedirect.com/science/article/pii/S2095311918619847 |
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