Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs
The purpose of this study was to screen key mRNAs and long non-coding RNAs (lncRNAs) that affect gonadal development in duck embryos and to explain scientifically gonadal development defects in the mulard duck. Three male embryonic gonadal tissues of the mulard duck (BF<sub>1</sub>, BF&l...
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Zhejiang University Press
2023-10-01
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| Series: | 浙江大学学报. 农业与生命科学版 |
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| Online Access: | https://www.academax.com/doi/10.3785/j.issn.1008-9209.2022.07.071 |
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| author | LI Li ZHANG Linli XIN Qingwu MIAO Zhongwei ZHU Zhiming QIU Junzhi HAO Xiaona HUANG Qinlou ZHENG Nenzhu |
| author_facet | LI Li ZHANG Linli XIN Qingwu MIAO Zhongwei ZHU Zhiming QIU Junzhi HAO Xiaona HUANG Qinlou ZHENG Nenzhu |
| author_sort | LI Li |
| collection | DOAJ |
| description | The purpose of this study was to screen key mRNAs and long non-coding RNAs (lncRNAs) that affect gonadal development in duck embryos and to explain scientifically gonadal development defects in the mulard duck. Three male embryonic gonadal tissues of the mulard duck (BF<sub>1</sub>, BF<sub>2</sub>, BF<sub>3</sub>) and the muscovy duck (F<sub>1</sub>, F<sub>2</sub>, F<sub>3</sub>) were collected to extract RNA and perform high-throughput sequencing, and differential genes and lncRNAs were screened to predict target genes and perform functional annotations. Finally, the sequencing data were verified by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). The results showed that a total of 1 109 differentially expressed genes were screened from the gonadal tissues of the mulard duck and the muscovy duck. Compared with the muscovy duck, 857 genes were up-regulated and 252 genes were down-regulated in the mulard duck. Among them, the aldo-keto reductase family 1 member D1 gene (AKR1D1), 17β-hydroxysteroid dehydrogenase 3 gene (17β-HSD3), and cholesterol side-chain cleavage enzyme gene (P450scc) may be related to gonadal differentiation and development in the mulard duck. Meanwhile, 733 significantly differentially expressed lncRNAs were obtained. Compared with the muscovy duck, a total of 660 lncRNAs were significantly up-regulated and 73 lncRNAs were significantly down-regulated in the mulard duck. Target gene prediction analysis showed that a total of 136 down-regulated lncRNAs and 893 up-regulated lncRNAs may be involved in differential gene expression and had potential regulatory relationships, among which, TCONS_00246198 targeted 17β-HSD3, and TCONS_00229529 targeted tetraspanin-2 gene (TSPAN2), suggesting that the above lncRNAs may participate in duck embryonic gonadal development by targeting key genes. The qRT-PCR results showed that the expression levels of differential genes and lncRNAs were consistent with the expression trends in transcriptome sequencing, indicating that the data obtained by high-throughput sequencing are relatively reliable. RNA binding protein immunoprecipitation (RIP) assay results revealed that compared with IgG, the enrichment level of TCONS_00246198 reached 71.51 times. The above results indicate that TCONS_00246198 interacts directly or indirectly with the 17β-HSD3 protein, which means that they may have a targeting relationship. In summary, this study obtains a batch of key mRNAs and lncRNAs that may affect duck embryonic gonadal development, and it is speculated that the differential lncRNAs can regulate the expression of differential genes. This study provides a scientific basis for understanding the differences in duck embryonic gonadal development and the mechanisms of avian gonadal development. |
| format | Article |
| id | doaj-art-cc5daadc48aa4ea0aaa5ef79c73d54fb |
| institution | DOAJ |
| issn | 1008-9209 2097-5155 |
| language | English |
| publishDate | 2023-10-01 |
| publisher | Zhejiang University Press |
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| series | 浙江大学学报. 农业与生命科学版 |
| spelling | doaj-art-cc5daadc48aa4ea0aaa5ef79c73d54fb2025-08-20T02:47:25ZengZhejiang University Press浙江大学学报. 农业与生命科学版1008-92092097-51552023-10-014972974310.3785/j.issn.1008-9209.2022.07.07110089209Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAsLI LiZHANG LinliXIN QingwuMIAO ZhongweiZHU ZhimingQIU JunzhiHAO XiaonaHUANG QinlouZHENG NenzhuThe purpose of this study was to screen key mRNAs and long non-coding RNAs (lncRNAs) that affect gonadal development in duck embryos and to explain scientifically gonadal development defects in the mulard duck. Three male embryonic gonadal tissues of the mulard duck (BF<sub>1</sub>, BF<sub>2</sub>, BF<sub>3</sub>) and the muscovy duck (F<sub>1</sub>, F<sub>2</sub>, F<sub>3</sub>) were collected to extract RNA and perform high-throughput sequencing, and differential genes and lncRNAs were screened to predict target genes and perform functional annotations. Finally, the sequencing data were verified by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). The results showed that a total of 1 109 differentially expressed genes were screened from the gonadal tissues of the mulard duck and the muscovy duck. Compared with the muscovy duck, 857 genes were up-regulated and 252 genes were down-regulated in the mulard duck. Among them, the aldo-keto reductase family 1 member D1 gene (AKR1D1), 17β-hydroxysteroid dehydrogenase 3 gene (17β-HSD3), and cholesterol side-chain cleavage enzyme gene (P450scc) may be related to gonadal differentiation and development in the mulard duck. Meanwhile, 733 significantly differentially expressed lncRNAs were obtained. Compared with the muscovy duck, a total of 660 lncRNAs were significantly up-regulated and 73 lncRNAs were significantly down-regulated in the mulard duck. Target gene prediction analysis showed that a total of 136 down-regulated lncRNAs and 893 up-regulated lncRNAs may be involved in differential gene expression and had potential regulatory relationships, among which, TCONS_00246198 targeted 17β-HSD3, and TCONS_00229529 targeted tetraspanin-2 gene (TSPAN2), suggesting that the above lncRNAs may participate in duck embryonic gonadal development by targeting key genes. The qRT-PCR results showed that the expression levels of differential genes and lncRNAs were consistent with the expression trends in transcriptome sequencing, indicating that the data obtained by high-throughput sequencing are relatively reliable. RNA binding protein immunoprecipitation (RIP) assay results revealed that compared with IgG, the enrichment level of TCONS_00246198 reached 71.51 times. The above results indicate that TCONS_00246198 interacts directly or indirectly with the 17β-HSD3 protein, which means that they may have a targeting relationship. In summary, this study obtains a batch of key mRNAs and lncRNAs that may affect duck embryonic gonadal development, and it is speculated that the differential lncRNAs can regulate the expression of differential genes. This study provides a scientific basis for understanding the differences in duck embryonic gonadal development and the mechanisms of avian gonadal development.https://www.academax.com/doi/10.3785/j.issn.1008-9209.2022.07.071mulard duckmuscovy duckgonadinfertilitylong non-coding RNAs (lncRNAs)mRNAs |
| spellingShingle | LI Li ZHANG Linli XIN Qingwu MIAO Zhongwei ZHU Zhiming QIU Junzhi HAO Xiaona HUANG Qinlou ZHENG Nenzhu Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs 浙江大学学报. 农业与生命科学版 mulard duck muscovy duck gonad infertility long non-coding RNAs (lncRNAs) mRNAs |
| title | Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs |
| title_full | Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs |
| title_fullStr | Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs |
| title_full_unstemmed | Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs |
| title_short | Combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non-coding RNAs and mRNAs |
| title_sort | combined analysis of embryonic gonadal development differences of mulard duck and muscovy duck using long non coding rnas and mrnas |
| topic | mulard duck muscovy duck gonad infertility long non-coding RNAs (lncRNAs) mRNAs |
| url | https://www.academax.com/doi/10.3785/j.issn.1008-9209.2022.07.071 |
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