基于转录组测序筛选黄牛低氧适应性相关差异基因

doi:10.7668/hbnxb.20190727

摘要/Abstract

摘要： 为探明藏黄牛对低氧适应的相关差异表达基因并分析差异表达基因功能和代谢通路，以藏黄牛和三江黄牛心脏组织为研究对象，提取总RNA，建立测序文库后利用Illumina HiSeqTM 4000进行测序，经生物信息学分析筛选出差异表达转录本，并对差异表达基因进行GO富集和KEGG通路分析，最后采用荧光定量PCR（RT-qPCR）验证测序数据的准确性。结果表明：藏黄牛相比于三江黄牛得到显著差异表达基因608个，其中上调基因467个，下调基因141个，推测表达量较高的B2M、COX7C、NFATC1、ECE1、CAST基因是与低氧适应性相关的基因；差异转录本GO功能富集分析可知，在分子功能、细胞组分、生物过程分别富集到327，253，2 191个条目，其中富集程度最高的条目分别是细胞发育过程、结合与转录因子活性、细胞前缘。KEGG分析结果表明，差异转录本显著富集在8条通路，筛选低氧适应性候选基因NFATC1是MP-PKG信号通路与T细胞受体信号通路成员，推测其通过cGMP-PKG通路与T细胞受体信号通路参与低氧适应性调控。采用高通量测序技术对藏黄牛和三江黄牛心脏组织进行转录组测序分析，获得大量差异表达基因，为研究动物低氧适应性机制奠定基础。

关键词: 黄牛, 心脏组织, 低氧适应性, 差异表达mRNA, 功能富集分析

Abstract: To identify differentially expressed genes related to hypoxia adaptation in Tibetan cattle and analyze differentially expressed gene functions and pathways,the total RNA was extracted from the heart tissues, then sequenced by Illumina HiSeqTM 4000. The differentially expressed transcripts were screened by bioinformatics analysis, GO and KEGG enrichment analysis were used to study the function of differentially expressed genes. The accuracy of RNA-Seq results was verified by RT-qPCR. The results showed that there were 608 significant differentially expressed genes in Tibetan cattle compared with Sanjiang cattle, including 467 up genes and 141 down genes. The B2M,COX7C,NFATC1,ECE1,CAST genes with high expression levels were inferred hypoxia-adapted related genes. Differential transcripts of GO function enrichment analysis revealed that molecular functions, cell components, and biological processes were enriched to 327 entries, 253 entries, and 2 191 entries, of which the most enriched entries were cell development process, binding and transcription factor activity, cell leading edge. KEGG analysis showed that the differential transcripts were significantly enriched in eight pathways, screening for the hypoxia-adaptive candidate gene NFATC1 was involved in the cGMP-PKG pathway and the T cell receptor signaling pathway, and was predicted to participate in hypoxia-adapted regulation through the cGMP-PKG pathway and the T cell receptor signaling pathway. RNA-seq technology was used to analyze the transcriptome of Tibetan cattle and Sanjiang cattle heart tissue, and a large number of differentially expressed genes were obtained, which laid a foundation for studying the hypoxia adaptation mechanism of animals.

Key words: Cattle, Heart tissue, Hypoxia adaptation, Differentially expressed mRNA, Functional enrichment analysis

中图分类号:

S823.8

侯孟典, 王会, 钟金城, 柴志欣, 益西康珠, 王吉坤, 王嘉博. 基于转录组测序筛选黄牛低氧适应性相关差异基因[J]. 华北农学报, 2020, 35(2): 217-227. doi: 10.7668/hbnxb.20190727.

HOU Mengdian, WANG Hui, ZHONG Jincheng, CHAI Zhixin, YIXI Kangzhu, WANG Jikun, WANG Jiabo. Screening Differential Genes Related to Hypoxia Adaptation in Cattle by Using Transcriptome Analysis[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2020, 35(2): 217-227. doi: 10.7668/hbnxb.20190727.

http://www.hbnxb.net/CN/Y2020/V35/I2/217

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