不同鸡种胚胎腿肌差异表达mRNA和lncRNA的筛选及其竞争性调控网络的构建

doi:10.11843/j.issn.0366-6964.2022.12.008

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (12): 4207-4220.doi: 10.11843/j.issn.0366-6964.2022.12.008

不同鸡种胚胎腿肌差异表达mRNA和lncRNA的筛选及其竞争性调控网络的构建

李洁^1,2, 赵瑞鹏^1,3, 陈楚雯^1,2, 杨朝武⁴, 吴锦波⁵, 李志雄^1,2*

1. 西南民族大学青藏高原动物遗传资源保护与利用教育部重点实验室, 成都 610041;
2. 西南民族大学畜牧兽医学院, 成都 610041;
3. 西南民族大学青藏高原研究院, 成都 610041;
4. 四川省畜牧科学研究院, 成都 610066;
5. 阿坝藏族羌族自治州畜牧科学技术研究所, 阿坝 624402

收稿日期:2022-05-23 出版日期:2022-12-23 发布日期:2022-12-25
通讯作者: 李志雄，主要从事家禽遗传育种研究，E-mail：lizhixiong@swun.edu.cn
作者简介:李洁(1999-)，女，山西洪洞人，硕士，主要从事分子生物学与畜禽育种研究，E-mail：1902548549@qq.com
基金资助:
四川省科技计划项目(2021YFYZ0031)；西南民族大学中央高校基本科研业务费专项资金项目(2022NYXXS036)

Screening of the Differentially Expressed mRNA and lncRNA and the Construction of Their Competitive Regulatory Network in Embryonic Leg Muscles of Different Chicken Breeds

LI Jie^1,2, ZHAO Ruipeng^1,3, CHEN Chuwen^1,2, YANG Chaowu⁴, WU Jinbo⁵, LI Zhixiong^1,2*

1. Key Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu 610041, China;
2. College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China;
3. Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China;
4. Sichuan Animal Science Academy, Chengdu 610066, China;
5. Institute of Science and Technology of Aba Tibetan and Qiang Autonomous Prefecture, Aba 624402, China

Received:2022-05-23 Online:2022-12-23 Published:2022-12-25

摘要/Abstract

摘要： 旨在筛选藏鸡和大恒肉鸡胚胎期骨骼肌差异表达的mRNA和lncRNA，并构建lncRNA-miRNA-mRNA竞争性调控网络，为进一步探讨两个鸡品种骨骼肌生长发育速度的差异机制奠定基础。随机选取已孵化18 d的藏鸡和大恒肉鸡胚胎各3个，采集胚胎腿肌组织进行转录组测序。筛选两个品种中差异表达的mRNAs和lncRNAs，对差异表达基因进行GO和KEGG富集分析，并对lncRNA的靶标miRNA以及靶向mRNA的miRNA进行预测，筛选与肌肉发育相关的mRNA和lncRNA构建lncRNA-miRNA-mRNA竞争性调控网络，最后利用实时荧光定量PCR (qRT-PCR)对测序结果进行验证。结果显示，共有106个mRNAs在两个品种中差异表达，其中上调表达mRNAs 48个，下调表达mRNAs 58个。差异表达lncRNAs共有28个，其中10个上调，18个下调。差异表达mRNA的GO富集结果显示，骨骼肌细胞分化条目被显著富集，KEGG富集分析中脂质代谢通路被显著富集。lncRNA靶基因的KEGG富集结果显示，在10个显著富集通路中，有基因显著富集于类固醇生物合成和脂肪酸生物合成等与脂质代谢相关的信号通路。筛选与骨骼肌发育相关的差异表达mRNAs和lncRNAs构建了骨骼肌发育相关的lncRNA-miRNA-mRNA调控网络，qRT-PCR结果显示其表达趋势与转录组测序结果一致，证实测序数据准确可靠。本研究筛选出藏鸡和大恒肉鸡胚胎期差异表达的mRNA和lncRNA，并构建了骨骼肌发育相关的lncRNA-miRNA-mRNA调控网络，为揭示不同鸡品种中骨骼肌生长发育的差异性提供理论依据。

关键词: 藏鸡, 大恒肉鸡, 转录组测序, 肌肉发育, 调控网络

Abstract: The objective of this study was to screen differentially expressed mRNAs (DEMs) and lncRNAs (DELs) in skeletal muscle of Tibetan chicken and Daheng broiler in the embryonic stage and construct a lncRNA-miRNA-mRNA regulation network, so as to provide a basis for further investigation of the difference mechanisms in skeletal muscle development between the two breeds. Three embryos of Tibetan chicken and Daheng broiler that has been incubated for 18 days were randomly selected, respectively. The embryonic leg muscle tissues were collected for trans-criptome sequencing. The DEMs and DELs were screened and verified by real-time quantitative PCR (qRT-PCR). The DEMs and DELs were performed by GO and KEGG enrichment analysis. The miRNA that not only as a target for lncRNA but also targeting mRNA were selected to construct a lncRNA-miRNA-mRNA regulatory network. The results showed that a total of 106 DEMs were screened in the two breeds, of which 48 mRNAs were up-regulated and 58 mRNAs were down-regulated. These DEMs significantly enriched in GO terms including skeletal muscle cell differentiation and KEGG pathways including lipid metabolism. Twenty eight DELs were screened, of which 10 lncRNAs were up-regulated and 18 lncRNAs were down-regulated. KEGG analysis of the target genes of lncRNAs showed that many target genes significantly enriched in signaling pathways related to lipid metabolisms, such as steroid biosynthesis and fatty acid biosynthesis. The DEMs and DELs associated with skeletal muscle development were screened and lncRNA-miRNA-mRNA competitive regulation network was constructed. The result of qRT-PCR showed that the expression trend of selected DEMs and DELs was consistent with the sequencing result. The DEMs and DELs related to skeletal muscle development of Tibetan chicken and Daheng broiler were screened to construct the lncRNA-miRNA-mRNA regulatory network. The study provided a theoretical basis for revealing the variability of skeletal muscle growth and development in different chicken breeds.

Key words: Tibetan chicken, Daheng broiler, transcriptome sequencing, muscle development, regulatory network

中图分类号:

S831.2

李洁, 赵瑞鹏, 陈楚雯, 杨朝武, 吴锦波, 李志雄. 不同鸡种胚胎腿肌差异表达mRNA和lncRNA的筛选及其竞争性调控网络的构建[J]. 畜牧兽医学报, 2022, 53(12): 4207-4220.

LI Jie, ZHAO Ruipeng, CHEN Chuwen, YANG Chaowu, WU Jinbo, LI Zhixiong. Screening of the Differentially Expressed mRNA and lncRNA and the Construction of Their Competitive Regulatory Network in Embryonic Leg Muscles of Different Chicken Breeds[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4207-4220.

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不同鸡种胚胎腿肌差异表达mRNA和lncRNA的筛选及其竞争性调控网络的构建

Screening of the Differentially Expressed mRNA and lncRNA and the Construction of Their Competitive Regulatory Network in Embryonic Leg Muscles of Different Chicken Breeds

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