Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig
Pigs’ backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism u...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/11/22/3654 |
| _version_ | 1797465282007007232 |
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| author | Xin Liu Weilong Tian Ligang Wang Longchao Zhang Jing Liang Lixian Wang |
| author_facet | Xin Liu Weilong Tian Ligang Wang Longchao Zhang Jing Liang Lixian Wang |
| author_sort | Xin Liu |
| collection | DOAJ |
| description | Pigs’ backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: <i>ELOVL5</i>, <i>SCD</i>, <i>DGAT2</i>, <i>SLC24A5,</i> and <i>TYRP1</i>, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies. |
| first_indexed | 2024-03-09T18:20:17Z |
| format | Article |
| id | doaj.art-1dd6c3caff084bdfa53dcb1742b85038 |
| institution | Directory Open Access Journal |
| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-09T18:20:17Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj.art-1dd6c3caff084bdfa53dcb1742b850382023-11-24T08:22:11ZengMDPI AGFoods2304-81582022-11-011122365410.3390/foods11223654Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black PigXin Liu0Weilong Tian1Ligang Wang2Longchao Zhang3Jing Liang4Lixian Wang5Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaCollege of Animal Science and Technology, Guangxi University, Nanning 530004, ChinaInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, ChinaPigs’ backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: <i>ELOVL5</i>, <i>SCD</i>, <i>DGAT2</i>, <i>SLC24A5,</i> and <i>TYRP1</i>, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.https://www.mdpi.com/2304-8158/11/22/3654pigsbackfat qualitymRNAslncRNAscandidate genes |
| spellingShingle | Xin Liu Weilong Tian Ligang Wang Longchao Zhang Jing Liang Lixian Wang Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig Foods pigs backfat quality mRNAs lncRNAs candidate genes |
| title | Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig |
| title_full | Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig |
| title_fullStr | Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig |
| title_full_unstemmed | Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig |
| title_short | Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig |
| title_sort | integrated analysis of long non coding rna and mrna to reveal putative candidate genes associated with backfat quality in beijing black pig |
| topic | pigs backfat quality mRNAs lncRNAs candidate genes |
| url | https://www.mdpi.com/2304-8158/11/22/3654 |
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