基于WGCNA与GSEA方法挖掘调控中卫山羊羊毛弯曲相关基因

doi:10.11843/j.issn.0366-6964.2022.09.011

摘要/Abstract

摘要： 旨在探究中卫山羊羊毛弯曲随生长发生变化的分子机制，挖掘不同发育时期影响羊毛弯曲度的关键基因。试验采集了3只中卫山羊出生后45日龄（弯曲毛）和365日龄（直毛）的皮肤组织，进行转录组测序（RNA-seq），使用WGCNA与GSEA分析找出Hub基因。以P-value<0.05和|log₂FoldChange|≥1作为差异表达基因筛选的标准，45日龄为对照组，365日龄为试验组共筛选得到1 252个显著差异表达基因，包括812个表达上调基因和440个下调基因。基于WGCNA方法分析共得到14个模块，其中黄色和绿松石模块与被毛弯曲表型相关。利用String和Cytoscape构建网络，筛选到20个影响羊毛弯曲度的核心基因。从GSEA结果中筛选的被显著富集通路Hedgehog signaling pathway、JAK/STAT signaling pathway、TGF/BETA signaling pathway等参与了毛囊发育调控。综合KEGG、WGCNA、分子网络构建、GSEA分析结果，共同筛选得到基因CCL27、IL7、WNT2，推断这3个基因在调控毛囊发育中起到了关键的调控作用。本研究为进一步阐明动物毛发弯曲的分子机制提供了理论基础。

关键词: 中卫山羊, 转录组测序, 羊毛弯曲, WGCNA, GSEA

Abstract: The purpose of this study was to explore the molecular mechanism of wool bending during growth of Zhongwei goat, and to explore the key genes affecting the curvature of wool at different developmental stages. The skin tissues of 3 Zhongwei goats at 45 days old (curved hair) and 365 days old (straight hair) were collected for transcriptome sequencing (RNA-seq). Hub gene was identified by WGCNA and GSEA analysis. Taking P-value<0.05 and log₂FoldChange ≥ 1 as the screening criteria for differentially expressed genes, a total of 1 252 significant differentially expressed genes were screened, the age of 45 days as the control group and 365 days as the experimental group, including 812 up-regulated genes and 440 down-regulated genes. A total of 14 modules were obtained based on WGCNA analysis, among which yellow and turquoise modules were related to the curved phenotype of coat. Network analysis indicated 20 core genes affecting wool curvature were screened using String and Cytoscape. GSEA results showed that Hedgehog signaling pathway, JAK/STAT signaling pathway, TGF/BETA signaling pathway and other regulatory pathways involved in hair follicle development were significantly enriched. Based on the results of KEGG, WGCNA, molecular network construction and GSEA analysis, the genes CCL27, IL7 and WNT2 were screened, and it was inferred that these genes played a key role in regulating hair follicle development. This study provides a theoretical basis for further elucidating the molecular mechanism of animal hair bending.

Key words: Zhongwei goat, transcriptome sequencing, wool bending, WGCNA, GSEA

中图分类号:

S827.2

李晓波, 刘占发, 刘悦, 陈倩, 马月辉, 赵倩君, 叶绍辉. 基于WGCNA与GSEA方法挖掘调控中卫山羊羊毛弯曲相关基因[J]. 畜牧兽医学报, 2022, 53(9): 2930-2943.

LI Xiaobo, LIU Zhanfa, LIU Yue, CHEN Qian, MA Yuehui, ZHAO Qianjun, YE Shaohui. Mining Genes Related to Wool Bending of Zhongwei Goat Based on WGCNA and GSEA[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2930-2943.

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