Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep
In the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected si...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01183/full |
| _version_ | 1818601840617455616 |
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| author | Deyin Zhang Xiaoxue Zhang Xiaoxue Zhang Fadi Li Fadi Li Fadi Li Chong Li Yongfu La Futao Mo Guoze Li Yukun Zhang Xiaolong Li Qizhi Song Yuan Zhao Weimin Wang |
| author_facet | Deyin Zhang Xiaoxue Zhang Xiaoxue Zhang Fadi Li Fadi Li Fadi Li Chong Li Yongfu La Futao Mo Guoze Li Yukun Zhang Xiaolong Li Qizhi Song Yuan Zhao Weimin Wang |
| author_sort | Deyin Zhang |
| collection | DOAJ |
| description | In the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected six lambs with very high (n = 3) and very low (n = 3) RFI values and analyzed their liver transcriptomes. A total of 101 differentially expressed genes were identified, of which 40 were upregulated and 61 were downregulated in the low-RFI group compared with that in the high-RFI group. The downregulated genes were mainly concentrated in immune function pathways, while the upregulated genes were mainly involved in energy metabolism pathways. Two differentially expressed genes, ADRA2A (encoding adrenoceptor alpha 2A) and RYR2 (ryanodine receptor 2), were selected as candidate genes for FE and subjected to single nucleotide polymorphism scanning and association analysis. Two synonymous mutations, ADRA2A g.1429 C > A and RYR2 g.1117 A > C, were detected, which were both significantly associated with the feed conversion rate. These findings provide a deeper understanding of the molecular mechanisms regulating FE, and reveal key genes and genetic variants that could be used to genetically improve FE in sheep. |
| first_indexed | 2024-12-16T12:57:47Z |
| format | Article |
| id | doaj.art-cf66b1d8510f4c8e8b4985d3fbe414cf |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-16T12:57:47Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-cf66b1d8510f4c8e8b4985d3fbe414cf2022-12-21T22:30:58ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-11-011010.3389/fgene.2019.01183480031Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu SheepDeyin Zhang0Xiaoxue Zhang1Xiaoxue Zhang2Fadi Li3Fadi Li4Fadi Li5Chong Li6Yongfu La7Futao Mo8Guoze Li9Yukun Zhang10Xiaolong Li11Qizhi Song12Yuan Zhao13Weimin Wang14College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaEngineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co. Ltd., Minqin, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaEngineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co. Ltd., Minqin, ChinaThe State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou, ChinaIn the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected six lambs with very high (n = 3) and very low (n = 3) RFI values and analyzed their liver transcriptomes. A total of 101 differentially expressed genes were identified, of which 40 were upregulated and 61 were downregulated in the low-RFI group compared with that in the high-RFI group. The downregulated genes were mainly concentrated in immune function pathways, while the upregulated genes were mainly involved in energy metabolism pathways. Two differentially expressed genes, ADRA2A (encoding adrenoceptor alpha 2A) and RYR2 (ryanodine receptor 2), were selected as candidate genes for FE and subjected to single nucleotide polymorphism scanning and association analysis. Two synonymous mutations, ADRA2A g.1429 C > A and RYR2 g.1117 A > C, were detected, which were both significantly associated with the feed conversion rate. These findings provide a deeper understanding of the molecular mechanisms regulating FE, and reveal key genes and genetic variants that could be used to genetically improve FE in sheep.https://www.frontiersin.org/article/10.3389/fgene.2019.01183/fullsheepfeed efficiencyresidual feed intakedifferentially expressed genesingle nucleotide polymorphism |
| spellingShingle | Deyin Zhang Xiaoxue Zhang Xiaoxue Zhang Fadi Li Fadi Li Fadi Li Chong Li Yongfu La Futao Mo Guoze Li Yukun Zhang Xiaolong Li Qizhi Song Yuan Zhao Weimin Wang Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep Frontiers in Genetics sheep feed efficiency residual feed intake differentially expressed gene single nucleotide polymorphism |
| title | Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep |
| title_full | Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep |
| title_fullStr | Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep |
| title_full_unstemmed | Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep |
| title_short | Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep |
| title_sort | transcriptome analysis identifies candidate genes and pathways associated with feed efficiency in hu sheep |
| topic | sheep feed efficiency residual feed intake differentially expressed gene single nucleotide polymorphism |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01183/full |
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