Identification of Salt-Related Co-expression Modules and Hub Genes in Lonicera japonica Based on WGCNA
Huang Luyao
Hou Congzhe
Liu Zhenhua
Duan Tongyao
Li Zhuangzhuang
Wang Bin
Li Jia
Abstract：Weighted gene co-expression network analysis(WGCNA)is a classic system biology analysis method,which could be used to identify co-expressed gene modules,explore the biological correlation between modules and target traits,and mining hub genes in the modules.In this study,15 sets of transcriptome data were collected from Lonicera japonica leaves treated with 300 mmol·L-1 NaCl for 0,12,24,48 and 72 hours.The WGCNA method was used to identify gene co-expression modules response to salt stress in L.japonica,and a total of 8 co-expression modules were obtained.The gene expression patterns of the Brown and Black modules showed a negative to positive trend with the extension of NaCl treatment time,and the correlation be-tween the two modules in module eigengene(ME)was relatively higher,indicating that the Brown and Black modules were salt-resistant specific modules in L.japonica.By calculating the connectivity of genes within the module,four hub genes in the Black module and ten hub genes in the Brown module were obtained.Function-al annotation suggested that these genes may play important roles in the salt resistant process of L.japonica.The results of relative gene expression analysis showed that the expression level of most hub genes were in-versely proportional to stress time,manifested as an increase in expression level at 12 hours of salt stress and then a decrease.The hub genes Ljap00036010,Ljap00006511,and Ljap00032341,whose expression levels significantly increased at 12 hours,were all involved in the plant photo response pathway,indicating that the hub genes may function in the early stage of salt stress response in L.japonica through rapid transcription,es-pecially in the rapid response of the photo response pathway.This study provided further understanding of the regulatory network of L.japonica in response to salt stress,which was of vital importance for breeding salt-tol-erant plants adapt to saline-alkali land,developing the honeysuckle industry and exploring and utilizing of sa-line-alkali land.However,the functions and mechanisms of the hub genes need to be further studied.
Keywords：Lonicera japonicaResponse to salt stressWeighted gene co-expression network analysis(WGCNA)Gene moduleHub genes
Publication Date：2025-09-30
Online Publishing Date：2026-05-22(First online date of this platform, not the publication date of the document)
Pages：13( 9-21 )