Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep
Tibetan sheep have developed unique adaptations for survival in the Qinghai–Tibet Plateau environment. However, the functional genes and molecular mechanisms that regulate hypoxia adaptation have not been fully characterized. In this study, based on the whole-genome resequencing data for Tibetan she...
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2024-11-01
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| author | Yufang Song Chao Yuan Xuejiao An Tingting Guo Wentao Zhang Zengkui Lu Jianbin Liu |
| author_facet | Yufang Song Chao Yuan Xuejiao An Tingting Guo Wentao Zhang Zengkui Lu Jianbin Liu |
| author_sort | Yufang Song |
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| description | Tibetan sheep have developed unique adaptations for survival in the Qinghai–Tibet Plateau environment. However, the functional genes and molecular mechanisms that regulate hypoxia adaptation have not been fully characterized. In this study, based on the whole-genome resequencing data for Tibetan sheep at different altitudes, the population differentiation index (<i>F</i><sub>ST</sub>) and nucleotide diversity ratio (θπ ratio) were evaluated in populations of 20 Oula sheep (3501 m altitude, OL), 20 Zashijia sheep (4369 m altitude, ZSJ), and 20 Awang sheep (4643 m altitude, AW) to reveal candidate loci related to high-altitude hypoxia. We screened 728 and 524 candidate genes in the AW vs. OL and ZSJ vs. OL groups, respectively, of which 134 genes were jointly screened. Candidate genes were mainly enriched in the Ras, melanoma, melanogenesis, VEGF, and PPAR signaling pathways. <i>HIF1AN</i>, <i>PDGFA</i>, <i>PDGFD</i>, <i>ANXA2</i>, <i>SOCS2</i>, <i>NOXA1</i>, <i>WNT7B</i>, <i>MMP14</i>, <i>GNG2</i>, <i>ATF6</i>, <i>PGAM2</i>, <i>PPP3R1</i>, <i>GSTCD</i>, and <i>PPARA</i> may play important roles in the high-altitude adaptation of Tibetan sheep. In conclusion, this study provides valuable insights into the genes and molecular mechanisms that underlie high-altitude hypoxia adaptation in Tibetan sheep. |
| format | Article |
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| series | Animals |
| spelling | doaj-art-a7223229c12340e7b8df49b377e5fb3f2025-08-20T01:53:37ZengMDPI AGAnimals2076-26152024-11-011422321210.3390/ani14223212Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan SheepYufang Song0Chao Yuan1Xuejiao An2Tingting Guo3Wentao Zhang4Zengkui Lu5Jianbin Liu6Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaTibetan sheep have developed unique adaptations for survival in the Qinghai–Tibet Plateau environment. However, the functional genes and molecular mechanisms that regulate hypoxia adaptation have not been fully characterized. In this study, based on the whole-genome resequencing data for Tibetan sheep at different altitudes, the population differentiation index (<i>F</i><sub>ST</sub>) and nucleotide diversity ratio (θπ ratio) were evaluated in populations of 20 Oula sheep (3501 m altitude, OL), 20 Zashijia sheep (4369 m altitude, ZSJ), and 20 Awang sheep (4643 m altitude, AW) to reveal candidate loci related to high-altitude hypoxia. We screened 728 and 524 candidate genes in the AW vs. OL and ZSJ vs. OL groups, respectively, of which 134 genes were jointly screened. Candidate genes were mainly enriched in the Ras, melanoma, melanogenesis, VEGF, and PPAR signaling pathways. <i>HIF1AN</i>, <i>PDGFA</i>, <i>PDGFD</i>, <i>ANXA2</i>, <i>SOCS2</i>, <i>NOXA1</i>, <i>WNT7B</i>, <i>MMP14</i>, <i>GNG2</i>, <i>ATF6</i>, <i>PGAM2</i>, <i>PPP3R1</i>, <i>GSTCD</i>, and <i>PPARA</i> may play important roles in the high-altitude adaptation of Tibetan sheep. In conclusion, this study provides valuable insights into the genes and molecular mechanisms that underlie high-altitude hypoxia adaptation in Tibetan sheep.https://www.mdpi.com/2076-2615/14/22/3212high-altitude adaptationTibetan sheep<i>F</i><sub>ST</sub>θπ ratioselection signal |
| spellingShingle | Yufang Song Chao Yuan Xuejiao An Tingting Guo Wentao Zhang Zengkui Lu Jianbin Liu Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep Animals high-altitude adaptation Tibetan sheep <i>F</i><sub>ST</sub> θπ ratio selection signal |
| title | Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep |
| title_full | Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep |
| title_fullStr | Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep |
| title_full_unstemmed | Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep |
| title_short | Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep |
| title_sort | genome wide selection signals reveal candidate genes associated with plateau adaptation in tibetan sheep |
| topic | high-altitude adaptation Tibetan sheep <i>F</i><sub>ST</sub> θπ ratio selection signal |
| url | https://www.mdpi.com/2076-2615/14/22/3212 |
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