Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken
Systematically constructing a gene expression atlas of poultry tissues is critically important for advancing poultry research and production. In this study, the gene expression profiles of 9 major tissues of Lueyang black-bone chicken were successfully constructed by transcriptome sequencing technol...
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Elsevier
2025-04-01
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| Series: | Poultry Science |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0032579125002251 |
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| author | Pan Li Yufei Yang Bo Ning Yingmin Tian Ling Wang Wenxian Zeng Hongzhao Lu Tao Zhang |
| author_facet | Pan Li Yufei Yang Bo Ning Yingmin Tian Ling Wang Wenxian Zeng Hongzhao Lu Tao Zhang |
| author_sort | Pan Li |
| collection | DOAJ |
| description | Systematically constructing a gene expression atlas of poultry tissues is critically important for advancing poultry research and production. In this study, the gene expression profiles of 9 major tissues of Lueyang black-bone chicken were successfully constructed by transcriptome sequencing technology. Through in-depth analysis of transcriptome data, a total of 10 housekeeping genes (HKGs) and 87 marker genes (MGs) were identified. Furthermore, by applying weighted gene co-expression network analysis (WGCNA), we delineated nine tissue-specific modules and 90 hub genes, offering novel insights into the regulatory networks underlying tissue-specific gene expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that HKGs were predominantly involved in maintaining fundamental cellular functions, with significant enrichment in pathways related to oxidative phosphorylation, cell cycle regulation, and DNA replication. MGs were closely associated with tissue-specific physiological functions, providing valuable insights into the molecular mechanisms governing tissue functionality. Notably, through multidimensional validation, EEF1A1 and FTH1 were confirmed to exhibit cross-tissue expression stability, establishing them as ideal reference genes for multi-tissue qPCR experiments in chickens. Additionally, we successfully identified tissue marker genes, including TNNT2, PIT54, SFTPC, and PGM1, which are specific to the heart, liver, lung, and breast muscle, respectively. The results of this study have important scientific value in expanding reference gene selection and elucidating tissue-specific molecular mechanisms, and provide solid theoretical support and technical guidance for poultry breeding improvement and production practice optimization. |
| format | Article |
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| institution | OA Journals |
| issn | 0032-5791 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Elsevier |
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| series | Poultry Science |
| spelling | doaj-art-5d5f9e100e8d4b4392a0d8cea141b65f2025-08-20T02:04:38ZengElsevierPoultry Science0032-57912025-04-01104410498610.1016/j.psj.2025.104986Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chickenPan Li0Yufei Yang1Bo Ning2Yingmin Tian3Ling Wang4Wenxian Zeng5Hongzhao Lu6Tao Zhang7School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Mathematics and Computer Science, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, 723001 Hanzhong, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi University of Technology, 723001 Hanzhong, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, 723001 Hanzhong, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi University of Technology, 723001 Hanzhong, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, 723001 Hanzhong, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi University of Technology, 723001 Hanzhong, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, 723001 Hanzhong, ChinaSchool of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, 723001 Hanzhong, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C, Shaanxi University of Technology, 723001 Hanzhong, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, 723001 Hanzhong, China; Corresponding author at: School of Biological Science and Engineering, Shaanxi University of Technology, 723001 Hanzhong, China.Systematically constructing a gene expression atlas of poultry tissues is critically important for advancing poultry research and production. In this study, the gene expression profiles of 9 major tissues of Lueyang black-bone chicken were successfully constructed by transcriptome sequencing technology. Through in-depth analysis of transcriptome data, a total of 10 housekeeping genes (HKGs) and 87 marker genes (MGs) were identified. Furthermore, by applying weighted gene co-expression network analysis (WGCNA), we delineated nine tissue-specific modules and 90 hub genes, offering novel insights into the regulatory networks underlying tissue-specific gene expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that HKGs were predominantly involved in maintaining fundamental cellular functions, with significant enrichment in pathways related to oxidative phosphorylation, cell cycle regulation, and DNA replication. MGs were closely associated with tissue-specific physiological functions, providing valuable insights into the molecular mechanisms governing tissue functionality. Notably, through multidimensional validation, EEF1A1 and FTH1 were confirmed to exhibit cross-tissue expression stability, establishing them as ideal reference genes for multi-tissue qPCR experiments in chickens. Additionally, we successfully identified tissue marker genes, including TNNT2, PIT54, SFTPC, and PGM1, which are specific to the heart, liver, lung, and breast muscle, respectively. The results of this study have important scientific value in expanding reference gene selection and elucidating tissue-specific molecular mechanisms, and provide solid theoretical support and technical guidance for poultry breeding improvement and production practice optimization.http://www.sciencedirect.com/science/article/pii/S0032579125002251Lueyang black-bone chickenRNA-seqMarker geneHousekeeping geneTissue specific gene |
| spellingShingle | Pan Li Yufei Yang Bo Ning Yingmin Tian Ling Wang Wenxian Zeng Hongzhao Lu Tao Zhang Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken Poultry Science Lueyang black-bone chicken RNA-seq Marker gene Housekeeping gene Tissue specific gene |
| title | Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken |
| title_full | Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken |
| title_fullStr | Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken |
| title_full_unstemmed | Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken |
| title_short | Transcriptome analysis of multiple tissues and identification of tissue-specific genes in Lueyang black-bone chicken |
| title_sort | transcriptome analysis of multiple tissues and identification of tissue specific genes in lueyang black bone chicken |
| topic | Lueyang black-bone chicken RNA-seq Marker gene Housekeeping gene Tissue specific gene |
| url | http://www.sciencedirect.com/science/article/pii/S0032579125002251 |
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