Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks
Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with hig...
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MDPI AG
2022-05-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/10/1256 |
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| author | Chunyan Yang Zhixiu Wang Qianqian Song Bingqiang Dong Yulin Bi Hao Bai Yong Jiang Guobin Chang Guohong Chen |
| author_facet | Chunyan Yang Zhixiu Wang Qianqian Song Bingqiang Dong Yulin Bi Hao Bai Yong Jiang Guobin Chang Guohong Chen |
| author_sort | Chunyan Yang |
| collection | DOAJ |
| description | Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregulated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. <i>PPAPA</i>, <i>FOXO3</i>, <i>FASN</i>, <i>PNPLA2</i>, <i>FKBP5</i>, <i>TCF7L2</i>, <i>BMP2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>ZBTB16</i>, <i>SIRT</i>, <i>GYG2</i>, <i>NCOR1,</i> and <i>NR3C1</i> were involved in the regulation of abdominal fat deposition. <i>PNPLA2</i>, <i>TCF7L2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>BMP2</i>, <i>FKBP5</i>, <i>GYG2</i>, and <i>ZBTB16</i> were regulated by the lncRNAs TCONS_00038080, TCONS_0033547, TCONS_00066773, XR_001190174.3, XR_003492471.1, XR_003493494.1, XR_001192142.3, XR_002405656.2, XR_002401822.2, XR_003497063.1, and so on. This study lays foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks. |
| first_indexed | 2024-03-10T03:28:44Z |
| format | Article |
| id | doaj.art-d241359516134cc4added3651b92bf9d |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T03:28:44Z |
| publishDate | 2022-05-01 |
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| series | Animals |
| spelling | doaj.art-d241359516134cc4added3651b92bf9d2023-11-23T09:46:15ZengMDPI AGAnimals2076-26152022-05-011210125610.3390/ani12101256Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in DucksChunyan Yang0Zhixiu Wang1Qianqian Song2Bingqiang Dong3Yulin Bi4Hao Bai5Yong Jiang6Guobin Chang7Guohong Chen8Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, ChinaAbdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregulated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. <i>PPAPA</i>, <i>FOXO3</i>, <i>FASN</i>, <i>PNPLA2</i>, <i>FKBP5</i>, <i>TCF7L2</i>, <i>BMP2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>ZBTB16</i>, <i>SIRT</i>, <i>GYG2</i>, <i>NCOR1,</i> and <i>NR3C1</i> were involved in the regulation of abdominal fat deposition. <i>PNPLA2</i>, <i>TCF7L2</i>, <i>FGF2</i>, <i>LIFR</i>, <i>BMP2</i>, <i>FKBP5</i>, <i>GYG2</i>, and <i>ZBTB16</i> were regulated by the lncRNAs TCONS_00038080, TCONS_0033547, TCONS_00066773, XR_001190174.3, XR_003492471.1, XR_003493494.1, XR_001192142.3, XR_002405656.2, XR_002401822.2, XR_003497063.1, and so on. This study lays foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks.https://www.mdpi.com/2076-2615/12/10/1256duckabdominal fat depositionRNA-seqmRNAlncRNA |
| spellingShingle | Chunyan Yang Zhixiu Wang Qianqian Song Bingqiang Dong Yulin Bi Hao Bai Yong Jiang Guobin Chang Guohong Chen Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks Animals duck abdominal fat deposition RNA-seq mRNA lncRNA |
| title | Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks |
| title_full | Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks |
| title_fullStr | Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks |
| title_full_unstemmed | Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks |
| title_short | Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks |
| title_sort | transcriptome sequencing to identify important genes and lncrnas regulating abdominal fat deposition in ducks |
| topic | duck abdominal fat deposition RNA-seq mRNA lncRNA |
| url | https://www.mdpi.com/2076-2615/12/10/1256 |
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