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Journal of Integrative Agriculture  2022, Vol. 21 Issue (8): 2384-2398    DOI: 10.1016/S2095-3119(21)63888-1
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Weighted gene co-expression network analysis identifies potential regulators in response to Salmonella Enteritidis challenge in the reproductive tract of laying ducks

ZHANG Yu1, 2, LUO Shu-wen2, HOU Li-e1, GU Tian-tian1, ZHU Guo-qiang2, Wanwipa VONGSANGNAK3, XU Qi1, CHEN Guo-hong1

1 Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225009, P.R.China

2 Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, P.R.China

3 Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand

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本研究以蛋鸭生殖道感染肠炎沙门氏菌为模型,采用加权基因共表达网络分析(Weighted Gene Co-expression Network Analysis, WGCNA)方法构建蛋鸭感染肠炎沙门氏菌生殖道应答共表达基因模块,筛选关键调控因子。结果表明,绍鸭感染肠炎沙门氏菌后,其中22%的鸭在生殖道的卵巢基质、小卵泡、输卵管峡部和阴道等多个组织定植。通过加权基因共表达网络(WGCNA)方法鉴定得到11个基因模块,并与组织载菌数据进行关联分析,筛选到3个与肠炎沙门氏菌生殖道感染应答高度相关的关键基因模块(P<0.01),包括185个共表达的差异表达基因(|log2FoldChange|>2,P<0.05),获得60个关键调控基因和125个转录因子。选取关键模块中连接度最高的免疫调控相关的14个枢纽基因(hub gene)进一步进行验证分析,结合基因功能,确定其中3个枢纽基因(TRAF3CXCR4IL13RA1)肠炎沙门氏菌应答关键调控因子,且主要通过NF-kappaB、Toll样受体、类固醇生物合成和p53信号通路等通路与其他基因共同发挥抗菌作用。以上研究结果不仅从理论上丰富肠炎沙门氏菌感染过程中的免疫调控网络关系的认识,同时也为培育肠炎沙门氏菌抗性品系提供潜在候选分子标志。


Salmonella Enteritidis (SE) is a zoonotic and vertically transmitted pathogen, often colonized in the reproductive tract of adult poultry, which can result in direct contamination of eggs and threaten human health.  Previous studies have revealed that some pattern recognition receptors and resistance genes were involved in regulating immune responses to SE invasion in birds.  However, the role of these immune response genes was not independent, and the interactions among the genes remained to be further investigated.  In this study, SE burden and colonization were determined in reproductive tissue after the ducks were SE-infected, and RNA-sequencing was performed to construct co-expression networks by weighted gene co-expression network analysis (WGCNA).  The result showed that SE could be isolated from 22% of infected-birds in any segment of the reproductive tract and the SE was readily colonized in the stroma, small follicle, isthmus, and vagina of the reproductive tracts in morbid ducks.  The top central, highly connected genes were subsequently identified three specific modules in the above four tissues at the defined cut-offs (P<0.01), including 60 new candidate regulators and 125 transcription factors.  Moreover, those 185 differentially expressed genes (DEGs) in these modules were co-expressed.  Moreover, the hub genes (TRAF3, CXCR4 and IL13RA1) were identified to act with many other genes through immune response pathways including NF-kappaB, Toll-like receptor, steroid biosynthesis, and p53 signaling pathways.  These data provide references that will understand the immune regulatory relationships during SE infection, but also assist in the breeding of SE-resistant lines through potential biomarkers.

Keywords:  duck        Salmonella Enteritidis        reproductive tract        infection-related genes        WGCNA  
Received: 19 February 2021   Accepted: 28 February 2022
Fund: This study was supported by the National Natural Science Foundation of China (31702107) and the Open Project Program of Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, China (JILAR-KF202018).
About author:  ZHANG Yu, Mobile: +86-18205271588, E-mail:; Correspondence XU Qi, E-mail:; CHEN Guo-hong, E-mail:

Cite this article: 

ZHANG Yu, LUO Shu-wen, HOU Li-e, GU Tian-tian, ZHU Guo-qiang, Wanwipa VONGSANGNAK, XU Qi, CHEN Guo-hong. 2022. Weighted gene co-expression network analysis identifies potential regulators in response to Salmonella Enteritidis challenge in the reproductive tract of laying ducks. Journal of Integrative Agriculture, 21(8): 2384-2398.

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