雷琼牛与陆丰牛背最长肌lncRNA表达特点及其相关ceRNA网络分析

doi:10.11843/j.issn.0366-6964.2023.05.017

摘要/Abstract

摘要： 旨在筛选雷琼牛与陆丰牛背最长肌差异表达lncRNAs、miRNAs以及mRNAs,通过构建lncRNA-miRNA-mRNA的竞争调控网络、搜寻lncRNA顺式靶向调控基因并进行功能预测,挖掘可供提升华南地区地方品种黄牛肉用价值的关键候选基因。本研究随机选取4月龄雌性雷琼牛与陆丰牛各4头,取背最长肌组织用于RNA测序,测序结果使用RT-qPCR验证。筛选两品种黄牛背最长肌差异表达lncRNAs、miRNAs和mRNAs,用于构建差异表达转录本的竞争调控网络以及搜寻lncRNA顺式靶向调控基因。候选基因使用GO和KEGG富集分析进行功能预测。结果表明,以雷琼牛为对照组,两个品种中存在119个差异表达的lncRNAs,其中73个上调表达,46个下调表达;差异表达的miRNAs共有13个,其中7个上调表达,6个下调表达;差异表达的mRNAs共有599个,其中155个上调表达,444个下调表达。竞争性调控网络中mRNAs的GO富集结果显示,与肌生成相关的条目主要为磷酸化以及膜结构等,KEGG富集结果中与肌生成相关的通路主要为Rap1、MAPK、PI3K-Akt等信号通路。顺式靶向调控基因的GO富集分析显示,与肌生成相关的GO条目主要为肌肉结构的发展、肌肉器官的发育等,KEGG富集结果中与肌生成相关的通路主要为MAPK信号传导途径以及局部粘附等。本研究筛选了雷琼牛与陆丰牛背最长肌差异表达lncRNAs、miRNAs以及mRNAs,构建了竞争调控网络并搜寻了lncRNA的顺式靶向调控基因,为进一步对华南地区地方品种黄牛肉用价值进行合理的开发与利用提供理论支持。

关键词: 陆丰牛, 雷琼牛, 背最长肌, lncRNA, ceRNA网络

Abstract: The aim of this study was to screen for differentially expressed lncRNAs, miRNAs and mRNAs in the longissimus dorsi of Leiqiong and Lufeng cattle, construct a competitive lncRNA-miRNA-mRNA regulatory network, search for lncRNA cis-targeted regulatory genes, then performed functional prediction to identify key candidate genes that could be used to enhance the utility value of local yellow beef breeds in South China. Four 4-month-old female Leiqiong cattle and four Lufeng cattle were randomly selected, and longissimus dorsi tissues were taken for RNA sequencing, and the sequencing results were verified using RT-qPCR. The differentially expressed lncRNAs, miRNAs and mRNAs were screened for the construction of a competitive regulatory network and the search for lncRNA cis-targeted regulatory genes. Candidate genes were used for functional prediction using GO and KEGG enrichment analysis. The results showed that, using Leiqiong cattle as the control group, there were 119 differentially expressed lncRNAs in the two breeds, of which 73 were up-regulated and 46 were down-regulated; a total of 13 differentially expressed miRNAs, of which 7 were up-regulated and 6 were down-regulated; and a total of 599 differentially expressed mRNAs, of which 155 were up-regulated and 444 were down-regulated. The GO enrichment analysis of mRNAs in the competitive regulatory network showed that the terms related to myogenesis were mainly phosphorylation and membrane structure. The pathways related to myogenesis in the KEGG enrichment analysis results were mainly signaling pathways such as Rap1, MAPK, PI3K-Akt, etc. The GO enrichment analysis of cis-targeted regulatory genes showed that the GO terms related to myogenesis were mainly the development of muscle structure and muscle organ development, etc. The pathways related to myogenesis in the KEGG enrichment results were mainly MAPK signaling pathways and local adhesion, etc.In this study, we screened the differentially expressed lncRNAs, miRNAs and mRNAs in the longissimus dorsi of Leiqiong and Lufeng cattle, and then constructed a competitive regulatory network and searched for lncRNA cis-targeted regulatory genes. The results of the experiments provide theoretical support for further rational development and utilization of the local breeds of yellow cattle in South China.

Key words: Lufeng cattle, Leiqiong cattle, longissimus dorsi, lncRNA, ceRNA networks

中图分类号:

S823.2

杨闯, 吴龙飞, 柳广斌, 李耀坤, 刘德武, 孙宝丽. 雷琼牛与陆丰牛背最长肌lncRNA表达特点及其相关ceRNA网络分析[J]. 畜牧兽医学报, 2023, 54(5): 1951-1963.

YANG Chuang, WU Longfei, LIU Guangbin, LI Yaokun, LIU Dewu, SUN Baoli. Expression Profile and Bioinformatics Analysis of lncRNA and Its Associated ceRNA Networks in Longissimus Dorsi from Lufeng Cattle and Leiqiong Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1951-1963.

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