利用加权基因共表达网络分析筛选天农麻鸡胴体性状候选基因

doi:10.11843/j.issn.0366-6964.2022.07.010

摘要/Abstract

摘要： 旨在通过转录组测序(RNA-Seq)与加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)筛选慢速型黄羽肉鸡天农麻鸡胴体性状相关候选基因。本研究以104只天农麻鸡为素材，在126日龄时进行屠宰，测定胸肌重等7个胴体性状，采集胸肌组织进行RNA-Seq。基于RNA-Seq数据获得基因表达矩阵后，结合表型进行WGCNA分析，确定目标模块，筛选目标模块的枢纽基因，并分别进行KEGG通路富集、蛋白质互作网络(protein-protein interaction network，PPI)构建和相关性分析。104份胸肌组织RNA-Seq质控后获得15 092个基因的表达量。与胴体表型进行WGCNA，共得到19个模块，其中4个模块与胴体性状极显著相关。功能富集结果表明，目标模块内基因主要富集在ECM-受体相互作用、黏着力等通路。以|Module membership|> 0.8、|Gene significance|> 0.2为标准筛选到58个枢纽基因，并通过PPI网络构建鉴定到5个网络节点基因，整合相关性分析确定COL1A2和SPARC为最重要候选基因。本研究通过大样本量转录组分析，发现ECM-受体相互作用等通路在天农麻鸡胴体性状调控中发挥主要作用，筛选到COL1A2和SPARC是影响全净膛率性状的重要候选基因，研究结果为鉴定选育分子标记，解析胴体性状分子机制奠定理论基础，为慢速型黄羽肉鸡育种提供重要参考。

关键词: 天农麻鸡, 胴体性状, 转录组测序, WGCNA

Abstract: The purpose of this study was to screen candidate genes for carcass traits of slow-growing yellow-feather broiler (Tiannong partridge chickens) by transcriptome sequencing (RNA-Seq) and weighted gene co-expression network analysis (WGCNA). The total of 104 Tiannong partridge chickens were slaughtered at 126 days of age. The 7 carcass traits including breast muscle weight were measured, and breast muscle tissues were collected for RNA-Seq. After obtaining the gene expression matrix based on RNA-Seq data, combined with the phenotype, WGCNA was carried out to determine the target module, screen the hub genes of the target module. KEGG pathway enrichment, protein-protein interaction network (PPI) construction and correlation analysis were carried out, respectively. The 15 092 genes were expressed in 104 breast muscle tissues after RNA-Seq quality control. By WGCNA of carcass phenotype, 19 modules were obtained, of which 4 modules were extremely significantly correlated with carcass traits. The results of functional enrichment showed that genes in the target modules were mainly enriched in ECM-receptor interaction, focal adhesion and other pathways. The 58 hub genes were screened according to|Module membership|> 0.8,|Gene significance|> 0.2. The 5 network node genes were identified through PPI network construction. By integrating correlation analysis, COL1A2 and SPARC were identified as the most important candidate genes. This study found that ECM-receptor interaction and other pathways played a major role in the regulation of carcass traits of Tiannong partridge chickens through large-scale transcriptome analysis. COL1A2 and SPARC are selected as important candidate genes affecting the percentage of eviscerated yield. The results lay a theoretical foundation for identifying molecular markers and analyzing the molecular mechanism of carcass traits, and provide an important reference for the breeding of slow-growing yellow- feather broilers.

Key words: Tiannong partridge chickens, carcass traits, RNA-Seq, WGCNA

中图分类号:

S831.2

赵迪, 康慧敏, 谭晓冬, 刘冉冉, 张正芬, 李华, 赵桂苹. 利用加权基因共表达网络分析筛选天农麻鸡胴体性状候选基因[J]. 畜牧兽医学报, 2022, 53(7): 2130-2140.

ZHAO Di, KANG Huimin, TAN Xiaodong, LIU Ranran, ZHANG Zhengfen, LI Hua, ZHAO Guiping. Screening of Candidate Genes for Carcass Traits of Tiannong Partridge Chicken Using Weighted Gene Co-expression Network Analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(7): 2130-2140.

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