Identification of the hub genes related to adipose tissue metabolism of bovine
Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding eff...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2022.1014286/full |
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| author | Xiaohui Wang Jianfang Wang Sayed Haidar Abbas Raza Jiahan Deng Jing Ma Xiaopeng Qu Shengchen Yu Dianqi Zhang Ahmed Mohajja Alshammari Hailah M. Almohaimeed Linsen Zan Linsen Zan |
| author_facet | Xiaohui Wang Jianfang Wang Sayed Haidar Abbas Raza Jiahan Deng Jing Ma Xiaopeng Qu Shengchen Yu Dianqi Zhang Ahmed Mohajja Alshammari Hailah M. Almohaimeed Linsen Zan Linsen Zan |
| author_sort | Xiaohui Wang |
| collection | DOAJ |
| description | Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality. |
| first_indexed | 2024-04-12T10:54:21Z |
| format | Article |
| id | doaj.art-7e6a5c2e5b354815bfddb93174ecb8fe |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-04-12T10:54:21Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj.art-7e6a5c2e5b354815bfddb93174ecb8fe2022-12-22T03:36:08ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692022-11-01910.3389/fvets.2022.10142861014286Identification of the hub genes related to adipose tissue metabolism of bovineXiaohui Wang0Jianfang Wang1Sayed Haidar Abbas Raza2Jiahan Deng3Jing Ma4Xiaopeng Qu5Shengchen Yu6Dianqi Zhang7Ahmed Mohajja Alshammari8Hailah M. Almohaimeed9Linsen Zan10Linsen Zan11College of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaDepartment of Biology, College of Science, University of Hail, Ha'il, Saudi ArabiaDepartment of Basic Science, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi ArabiaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaNational Beef Cattle Improvement Center, Northwest A&F University, Xianyang, ChinaDue to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality.https://www.frontiersin.org/articles/10.3389/fvets.2022.1014286/fulldifferent dietsWGCNAlipid metabolismenergy metabolismhub genes |
| spellingShingle | Xiaohui Wang Jianfang Wang Sayed Haidar Abbas Raza Jiahan Deng Jing Ma Xiaopeng Qu Shengchen Yu Dianqi Zhang Ahmed Mohajja Alshammari Hailah M. Almohaimeed Linsen Zan Linsen Zan Identification of the hub genes related to adipose tissue metabolism of bovine Frontiers in Veterinary Science different diets WGCNA lipid metabolism energy metabolism hub genes |
| title | Identification of the hub genes related to adipose tissue metabolism of bovine |
| title_full | Identification of the hub genes related to adipose tissue metabolism of bovine |
| title_fullStr | Identification of the hub genes related to adipose tissue metabolism of bovine |
| title_full_unstemmed | Identification of the hub genes related to adipose tissue metabolism of bovine |
| title_short | Identification of the hub genes related to adipose tissue metabolism of bovine |
| title_sort | identification of the hub genes related to adipose tissue metabolism of bovine |
| topic | different diets WGCNA lipid metabolism energy metabolism hub genes |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2022.1014286/full |
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