Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia
Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these...
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| Format: | Article |
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Frontiers Media S.A.
2019-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00244/full |
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| author | Grace Lin Grace Lin Natascha M. Thevasagayam Z. Y. Wan Z. Y. Wan B. Q. Ye Gen Hua Yue Gen Hua Yue Gen Hua Yue |
| author_facet | Grace Lin Grace Lin Natascha M. Thevasagayam Z. Y. Wan Z. Y. Wan B. Q. Ye Gen Hua Yue Gen Hua Yue Gen Hua Yue |
| author_sort | Grace Lin |
| collection | DOAJ |
| description | Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage. |
| first_indexed | 2024-12-13T11:31:06Z |
| format | Article |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T11:31:06Z |
| publishDate | 2019-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-fabf3c1d32204138b012559f9405d02f2022-12-21T23:47:56ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-03-011010.3389/fgene.2019.00244421872Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline TilapiaGrace Lin0Grace Lin1Natascha M. Thevasagayam2Z. Y. Wan3Z. Y. Wan4B. Q. Ye5Gen Hua Yue6Gen Hua Yue7Gen Hua Yue8Temasek Life Sciences Laboratory, National University of Singapore, Singapore, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore, SingaporeTemasek Life Sciences Laboratory, National University of Singapore, Singapore, SingaporeTemasek Life Sciences Laboratory, National University of Singapore, Singapore, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore, SingaporeTemasek Life Sciences Laboratory, National University of Singapore, Singapore, SingaporeTemasek Life Sciences Laboratory, National University of Singapore, Singapore, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeGrowth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage.https://www.frontiersin.org/article/10.3389/fgene.2019.00244/fulltilapiagrowthmeat qualityRNAgene |
| spellingShingle | Grace Lin Grace Lin Natascha M. Thevasagayam Z. Y. Wan Z. Y. Wan B. Q. Ye Gen Hua Yue Gen Hua Yue Gen Hua Yue Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia Frontiers in Genetics tilapia growth meat quality RNA gene |
| title | Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia |
| title_full | Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia |
| title_fullStr | Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia |
| title_full_unstemmed | Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia |
| title_short | Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia |
| title_sort | transcriptome analysis identified genes for growth and omega 3 6 ratio in saline tilapia |
| topic | tilapia growth meat quality RNA gene |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00244/full |
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