Identification of Heat-responsive Co-expression Modules and Mining of Hub Genes in Maize Tassel Based on WGCNA

doi:10.13560/j.cnki.biotech.bull.1985.2025-1424

Abstract

Abstract:

Objective To identify hub genes closely associated with heat stress regulatory pathways and stress-resistance traits, and to provide new insights into the molecular mechanisms underlying heat tolerance in maize (Zea mays). Method A heat-tolerant inbred line, PHBA6, and a heat-sensitive inbred line, Ji63, were used as experimental materials. Plants were grown under both field and greenhouse conditions, and heat stress was imposed at the early flowering stage. Based on transcriptome sequencing, the molecular response characteristics of tassels from the two genotypes under heat stress were systematically compared. Result A total of 1 288 differentially expressed genes (DEGs) were identified in PHBA6, whereas 912 DEGs were detected in Ji63 under heat stress. Weighted gene co-expression network analysis (WGCNA) was further performed to construct gene co-expression networks associated with stress-resistance phenotypic traits, resulting in the identification of 15 gene modules significantly correlated with tassel heat tolerance. Among them, four modules showing the strongest correlations with target traits were selected, and a set of potential key genes was screened. These genes were mainly involved in biological processes such as transcriptional regulation, protein homeostasis maintenance, reactive oxygen species metabolism, and stress signal transduction. Conclusion This study systematically reveals the key regulatory network characteristics of maize tassels under heat stress and identifies a group of hub genes closely associated with heat tolerance and their potential regulatory pathways.

Key words: maize, heat stress, weighted gene co-expression network, transcriptome

QIN Tian-yuan, LYU Yu-ping, ABULAITI Abula, HAN Deng-Xu, DONG Yuan, ZHANG Xue, YANG Jie. Identification of Heat-responsive Co-expression Modules and Mining of Hub Genes in Maize Tassel Based on WGCNA[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1424.

Figures/Tables 11

Table 1 Experimental materials

自交系

Inbred line

母本

Maternal parent

父本

Paternal parent

Fig. 1 Differentially expressed genes in tassels of PHBA6 and J63 under different treatmentCK: Control. D: Stress

Fig. 2 Determination of soft thresholds for gene co-expression networks

Fig. 3 Correlation heatmap of gene co-expression network modules and traitsThe horizontal axis indicates different traits, and the vertical axis indicates the eigenvector of each module. Red grids indicate a positive correlation between traits and modules, while green grids indicate a negative correlation between traits and modules. PH: Plant height. EH: Ear height. ASI: Anthesis-silking interval. EL: Ear length ED: Ear diameter. Y: Yield

Fig. 4 Correlation of module eigengenes (ME) among different modules in the gene co-expression network

Fig. 5 GO enrichment of genes in candidate modulesA, B, C, and D refers to the GO enrichment analysis results of genes in the blue, brown, green, and turquoise modules, respectively. The color intensity indicates the significance level: the darker the red, the smaller the P-value (higher significance), while blue indicates a larger P-value (lower significance), the same below. The sizes of the dots indicate the number of enriched genes; the larger the dot, the greater the number of enriched genes

Fig. 6 KEGG enrichment of genes in candidate modulesA, B, C, and D refers to the KEGG enrichment analysis results of genes in the blue, brown, turquoise, and green modules, respectively

Fig. 7 Mining of gene co-expression networks and hub genes in candidate modulesA, B, C, and D indicate the brown, green, turquoise, and blue modules respectively; the "pink circles" indicate the core genes

Table 2 Functional annotation of hub genes in different modules

模块 Module	核心基因 Hub gene	拟南芥同源基因 Homologous gene in A. thaliana	基因功能 Gene function
blue	Zm00001eb428210	AT5G47060	假设蛋白（DUF581） Hypothetical protein （DUF581）
blue	Zm00001eb070520	AT4G28815	碱性螺旋‒环‒螺旋（bHLH）DNA结合超家族蛋白 Basic helix-loop-helix （bHLH） DNA-binding superfamily protein
blue	Zm00001eb386130	AT5G64790	O-糖基水解酶家族17蛋白 O-Glycosyl hydrolases family 17 protein
blue	Zm00001eb301770	X	未知功能 Unknown
brown	Zm00001eb115900	X	未知功能 Unknown
brown	Zm00001eb010150	AT1G14710	富含羟脯氨酸的糖蛋白家族蛋白 Hydroxyproline-rich glycoprotein family protein
brown	Zm00001eb404090	X	转导蛋白家族蛋白/WD-40重复序列家族蛋白 Transducin family protein/WD-40 repeat family protein
brown	Zm00001eb070610	X	未知功能 Unknown
green	Zm00001eb380460	AT3G02380	CONSTANS类似蛋白2 CONSTANS-like 2
green	Zm00001eb229830	AT3G61350	SKP1相互作用伙伴4 SKP1 interacting partner 4
green	Zm00001eb235230	AT4G03030	半乳糖氧化酶/kelch重复超家族蛋白 Galactose oxidase/kelch repeat superfamily protein
green	Zm00001eb409030	X	未知功能 Unknown
green	Zm00001eb331670	X	未知功能 Unknown
green	Zm00001eb173270	AT1G32730	（1 of 1） PTHR35696：SF1-F6N18.11
turquoise	Zm00001eb252020	AT1G75330	鸟氨酸氨甲酰转移酶 Ornithine carbamoyltransferase
turquoise	Zm00001eb148420	AT1G56410	热休克70 kDa蛋白 Heat shock 70 kDa protein-like
turquoise	Zm00001eb031560	AT2G43010	编码一个与活性PhyB蛋白相互作用的核定位bHLH蛋白 Encodes a nuclear localized bHLH protein that interacts with active PhyB protein
turquoise	Zm00001eb304350	X	未知功能 Unknown

Fig. 8 Cross-validation of hub genes by RT-qPCR and RNA-seqA: Ji63; B: PHBA6

Fig. 9 Subcellular localization of the ZmPIF4 protein in Z. mays

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