Transcriptomic Analysis of Maize Root and Leaf Responses to Heat Stress at the Seedling Stage

Abstract

Acute thermal stress severely limits maize (Zea mays) productivity, requiring a systemic understanding of organ-specific adaptive mechanisms. This study integrated transcriptomic data from two independent BioProjects, PRJNA1335774 (root) and PRJNA947789 (leaf), to delineate the molecular responses of maize seedlings to heat. A rigorous bioinformatic pipeline was employed, involving trimmomatic for quality control, HISAT2 for genomic alignment, and pheatmap for hierarchical clustering. Principal component analysis (PCA) revealed that heat stress at 42 ^oC was the primary driver of transcriptional variation, explaining 92% of the variance in roots and 80% in leaves, significantly outweighing tissue-specific signatures. Volcano plots identified thousands of high-confidence differentially expressed genes (DEGs) with extreme statistical significance. Hierarchical clustering confirmed a massive "transcriptional reset," characterized by the induction of a conserved heat-stress response (HSR) module and the simultaneous suppression of primary metabolic pathways. While the systemic response was dominant, roots exhibited a more synchronized molecular shift, whereas leaves showed higher secondary variability (16% on PC2), likely reflecting the complex demands of photosynthetic regulation. These findings demonstrate that maize seedlings prioritize cellular protection over growth through a coordinated growth-to-defense tradeoff. The identified DEGs and conserved modules provide robust genetic targets for molecular breeding and genome editing to enhance thermotolerance in maize cultivars.