Responses to Temperature Shocks in <i>Zymoseptoria tritici</i> Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation

Pathogens' responses to sudden temperature fluctuations, spanning various temporal scales, are critical determinants of their survival, growth, reproduction, and homeostasis. Here, we combined phenotyping, transcriptomics, and genome-wide association approaches to investigate how the wheat pathogen <i>Zymoseptoria tritici</i> responds to and recovers from temperature shocks. Survival emerged as the most significantly affected trait immediately following temperature shocks across 122 geographically diverse strains. In contrast, post-recovery phenotypic traits, including growth rate and melanization, showed no significant deviations from control conditions. Transcriptomic analyses of a reference strain revealed temperature stress-specific gene expression patterns, with genes involved in protein folding, redox homeostasis, membrane stabilization, and cell-wall remodeling playing central roles in the response. A multi-reference k-mer genome-wide association study identified six loci significantly associated with cold shock responses. Among these, two loci emerged as strong candidates for near-freezing temperature adaptation, including a 60S ribosomal protein gene involved in protein synthesis and stress recovery and an NADH oxidoreductase gene implicated in redox homeostasis and oxidative stress tolerance. These findings shed light on the distinct molecular strategies <i>Z. tritici</i> employs to adapt to temperature stress and provide novel insights into fungal resilience under dynamic environmental conditions. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.