Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens)

Bao Qi; Zhang Xiaolan; Bao Pengjia; Liang Chunnian; Guo Xian; Chu Min; Yan Ping

doi:10.1007/s13258-021-01137-5

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자료유형: 학술저널

저자정보: Bao Qi (Chinese Academy of Agricultural Sciences) Zhang Xiaolan (Chinese Academy of Agricultural Sciences) Bao Pengjia (Chinese Academy of Agricultural Sciences) Liang Chunnian (Chinese Academy of Agricultural Sciences) Guo Xian (Chinese Academy of Agricultural Sciences) Chu Min (Chinese Academy of Agricultural Sciences) Yan Ping (Chinese Academy of Agricultural Sciences)

저널정보: 한국유전학회 Genes & Genomics Genes & Genomics Vol.43 No.10

발행연도: 2021.10

수록면: 1,231 - 1,246 (16page)

DOI: 10.1007/s13258-021-01137-5

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연구주제

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연구배경

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Background As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. Objective Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great signifcance to identify the genetic characteristics and yak breeding. Methods Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze diferentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identifed and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. Results Our results revealed that 1098, 1429, and 1645 DEGs were identifed in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identifed 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The signifcant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. Conclusions In this study, we obtained two hypoxia-related specifc modules and identifed hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.

#Hypoxia adaptability #Bos grunniens #WGCNA #Hub gene

참고문헌 (69)

참고문헌 신청

Anders S / 2010 / Analysing RNA-Seq data with the DESeq package / Mol Biol

Heike Angerer / 2013 / The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins / Biochemical Society Transactions 41(5):1335~1341

Angerer H / 2014 / The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity / Proc Natl Acad Sci USA 111:5207~5212

Asma Babar / 2019 / Comparative iTRAQ Proteomics Identified Myocardium Proteins Associated with Hypoxia of Yak / Current Proteomics 16(4):314~329

Minlan Bai / 2016 / Relationships between interspecific differences in the mass of internal organs, biochemical markers of metabolic activity, and the thermogenic properties of three small passerines / Avian Research 7(1):11

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