基于WGCNA的玉米雄穗耐热相关共表达模块鉴定和核心基因发掘

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

摘要/Abstract

摘要：

目的挖掘玉米中与热胁迫调控通路、抗逆指标紧密相关的核心基因，为解析玉米耐热机理提供新方向。方法选用耐热性较强的自交系PHBA6和热敏感自交系吉63为材料，分别在田间和温室条件下种植，于开花前期实施热胁迫处理。基于转录组测序分析，系统比较热胁迫条件下2种基因型雄穗的分子响应特征。结果在PHBA6中共鉴定1 288个差异表达基因，在吉63中共鉴定到912个差异表达基因。进一步通过加权基因共表达网络分析（weighted gene co-expression network analysis, WGCNA）构建与抗逆表型性状相关的基因共表达网络，共鉴定出15个与雄穗耐热性显著相关的基因模块。其中，4个与目标性状相关性最高的模块中进一步筛选出一批潜在关键基因，这些基因主要涉及转录调控、蛋白稳态维持、活性氧代谢及胁迫信号转导等生物学过程。结论系统揭示了玉米雄穗在热胁迫下的关键调控网络特征，明确了一批与耐热性密切相关的核心基因及其潜在调控通路。

关键词: 玉米, 热胁迫, 加权基因共表达网络, 转录组学

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

秦天元, 吕玉平, 阿不来提·阿布拉, 韩登旭, 董远, 张雪, 杨杰. 基于WGCNA的玉米雄穗耐热相关共表达模块鉴定和核心基因发掘[J]. 生物技术通报, 2026, 42(10): 55-66.

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, 2026, 42(10): 55-66.

图/表 11

表1 试验材料

Table 1 Experimental materials

自交系

Inbred line

母本

Maternal parent

父本

Paternal parent

图1 不同处理下PHBA6与吉63雄穗中差异表达基因数CK：对照；D：胁迫

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

图2 基因共表达网络分析中软阈值的确定

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

图3 基因共表达网络模块与性状的关联热图横轴表示不同的性状，纵轴表示每一个模块的特征向量。红色的格子代表性状与模块具有正相关性，绿色的格子代表性状与模块具有负相关性。PH：株高；EH：穗位高；ASI：开花吐丝间隔期；EL：穗长；ED：穗粗；Y：产量

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

图4 基因共表达网络不同模块间ME的相关性

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

图5 候选模块中基因的GO富集A、B、C和D分别表示blue、brown、green和turquoise模块内基因的GO富集分析结果。颜色深浅表示显著性水平，红色越深表示P值越小（显著性越高），蓝色表示P值较大（显著性较低），下同。圆点大小表示富集基因的数量，圆越大，富集基因数目越多

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

图6 候选模块中基因的KEGG富集A、B、C和D分别表示blue、brown、turquoise和green模块内基因的KEGG富集分析结果

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

图7 候选模块中基因共表达网络及核心基因的挖掘A、B、C和D分别为brown、green、turquoise和blue模块；“粉红色圆”代表核心基因

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

表2 不同模块中核心基因的功能注释

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 kD蛋白 Heat shock 70 kD 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

图8 核心基因的RT-qPCR与RNA-seq交互验证

Fig. 8 Cross-validation of hub genes by RT-qPCR and RNA-seq

图9 玉米ZmPIF4蛋白的亚细胞定位

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

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