Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thicknes...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-06-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/9/6/313 |
| _version_ | 1811296385479213056 |
|---|---|
| author | Xin Liu Jianfei Gong Ligang Wang Xinhua Hou Hongmei Gao Hua Yan Fuping Zhao Longchao Zhang Lixian Wang |
| author_facet | Xin Liu Jianfei Gong Ligang Wang Xinhua Hou Hongmei Gao Hua Yan Fuping Zhao Longchao Zhang Lixian Wang |
| author_sort | Xin Liu |
| collection | DOAJ |
| description | Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (<i>AQP9</i>, <i>DKK3</i>, <i>GLYCTK</i>, <i>GLIPR1</i>, and <i>DUSP2</i>) related to fat deposition were found to be strong candidate genes, and mir-31-5p/<i>AQP9</i> and mir-31-5p/<i>GLIPR1</i> may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies. |
| first_indexed | 2024-04-13T05:48:34Z |
| format | Article |
| id | doaj.art-89ec3aed219b427f8cf090f72910836c |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-04-13T05:48:34Z |
| publishDate | 2019-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-89ec3aed219b427f8cf090f72910836c2022-12-22T02:59:53ZengMDPI AGAnimals2076-26152019-06-019631310.3390/ani9060313ani9060313Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in PigsXin Liu0Jianfei Gong1Ligang Wang2Xinhua Hou3Hongmei Gao4Hua Yan5Fuping Zhao6Longchao Zhang7Lixian Wang8Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaBackfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (<i>AQP9</i>, <i>DKK3</i>, <i>GLYCTK</i>, <i>GLIPR1</i>, and <i>DUSP2</i>) related to fat deposition were found to be strong candidate genes, and mir-31-5p/<i>AQP9</i> and mir-31-5p/<i>GLIPR1</i> may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies.https://www.mdpi.com/2076-2615/9/6/313backfat depositioncandidate geneexpression profilepigregulatory network |
| spellingShingle | Xin Liu Jianfei Gong Ligang Wang Xinhua Hou Hongmei Gao Hua Yan Fuping Zhao Longchao Zhang Lixian Wang Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs Animals backfat deposition candidate gene expression profile pig regulatory network |
| title | Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs |
| title_full | Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs |
| title_fullStr | Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs |
| title_full_unstemmed | Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs |
| title_short | Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs |
| title_sort | genome wide profiling of the microrna transcriptome regulatory network to identify putative candidate genes associated with backfat deposition in pigs |
| topic | backfat deposition candidate gene expression profile pig regulatory network |
| url | https://www.mdpi.com/2076-2615/9/6/313 |
| work_keys_str_mv | AT xinliu genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT jianfeigong genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT ligangwang genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT xinhuahou genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT hongmeigao genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT huayan genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT fupingzhao genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT longchaozhang genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs AT lixianwang genomewideprofilingofthemicrornatranscriptomeregulatorynetworktoidentifyputativecandidategenesassociatedwithbackfatdepositioninpigs |