Maize may be exposed to several abiotic stresses in the field. Therefore, identifying the tolerance mechanisms of naturally field stress is mandatory. Gene expression data of maize upon abiotic stress were collected, and 560 differentially expressed genes (DEGs) were identified through meta-analysis. The most significant gene ontology terms in up-regulated genes were “response to abiotic stress” and “chitinase activity”. “Phosphorelay signal transduction system” was the most significant enriched biological process in down-regulated DEGs. The co-expression analysis unveiled seven modules of DEGs, with a notable positive correlation between the modules and abiotic stress. Furthermore, the statistical significance was strikingly high for the turquoise, green, and yellow modules. The turquoise group played a central role in orchestrating crucial adaptations in metabolic and stress response pathways in maize when exposed to abiotic stress. Within three up-regulated modules, Zm.7361.1.A1_at, Zm.10386.1.A1_a_at, and Zm.10151.1.A1_at emerged as hub genes. These genes might introduce novel candidates implicated in stress tolerance mechanisms, warranting further comprehensive investigation and research. In parallel, the R package glmnet was applied to fit a logistic LASSO regression model on the DEGs profile to select candidate genes associated with abiotic responses in maize. The identified hub genes and LASSO regression genes were validated on an independent microarray dataset. Additionally, Differential Gene Correlation Analysis (DGCA) was performed on LASSO and hub genes to investigate the gene-gene regulatory relationship. The p-value of DGCA of 16 pairwise gene comparisons was lower than 0.01, indicating a gene-gene significant change in correlation between control and abiotic stress. Integrated WGCNA and logistic LASSO analysis revealed Zm.11185.1.S1_at, Zm.2331.1.S1_x_at, and Zm.17003.1.S1_at. Notably, these three genes were identified in the 16 gene-pair comparisons. This finding highlights the notable significance of these genes in the abiotic stress response. Additional research into maize stress tolerance may focus on these three genes.

中文翻译：

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玉米（Zea mays L.）基因共表达网络水平非生物胁迫反应的转录调查及差异基因相关分析

玉米在田间可能会受到多种非生物胁迫。因此，确定自然场应力的耐受机制是强制性的。收集了玉米非生物胁迫下的基因表达数据，并通过荟萃分析鉴定了560个差异表达基因（DEG）。上调基因中最重要的基因本体术语是“对非生物胁迫的响应”和“几丁质酶活性”。“磷酸中继信号转导系统”是下调DEGs中最重要的富集生物过程。共表达分析揭示了 DEG 的七个模块，这些模块与非生物胁迫之间存在显着的正相关。此外，绿松石色、绿色和黄色模块的统计显着性非常高。当玉米暴露于非生物胁迫时，绿松石组在协调代谢和胁迫反应途径的关键适应方面发挥了核心作用。在三个上调模块中，Zm.7361.1.A1_at、Zm.10386.1.A1_a_at 和 Zm.10151.1.A1_at 作为中心基因出现。这些基因可能会引入与应激耐受机制有关的新候选基因，值得进一步全面的调查和研究。同时，应用 R 包 glmnet 在 DEG 谱上拟合逻辑 LASSO 回归模型，以选择与玉米非生物反应相关的候选基因。确定的中心基因和 LASSO 回归基因在独立的微阵列数据集上进行了验证。此外，对 LASSO 和 hub 基因进行差异基因相关分析 (DGCA)，以研究基因与基因的调控关系。16 个配对基因比较的 DGCA p 值低于 0.01，表明对照和非生物胁迫之间的基因-基因相关性发生显着变化。综合 WGCNA 和逻辑 LASSO 分析显示 Zm.11185.1.S1_at、Zm.2331.1.S1_x_at 和 Zm.17003.1.S1_at。值得注意的是，这三个基因在 16 个基因对比较中被鉴定出来。这一发现凸显了这些基因在非生物胁迫反应中的显着重要性。对玉米胁迫耐受性的其他研究可能集中在这三个基因上。