Differential Modulation of Wheat Transcriptional Programs Driven by Native Endophytic Fungi.

Fungal endophytes are increasingly recognised as key modulators of plant physiology, however their molecular impact on major crops such as wheat (Triticum aestivum L.) remains underexplored. In this study, we analyzed the transcriptomic response of wheat seedlings to treatment with native endophytic fungi representing four species: Penicillium olsonii, Chrysosporium pseudomerdarium, Sarocladium spinificis, and Sarocladium strictum. Using high-resolution RNA-sequencing, we reveal that each endophyte induces a distinct transcriptional landscape in wheat seedlings grown under controlled conditions, reflecting divergent modes of host interaction. Penicillium olsonii and C. pseudomerdarium induced broad transcriptional reprogramming, characterised by repression of chromatin organisation and DNA replication pathways, coupled with selective activation of signalling and metabolic functions—suggesting a state of physiological priming or resource reallocation. Sarocladium spinificis triggered a moderate, predominantly upregulatory response involving circadian rhythm, ABA signalling, and stress-associated pathways, consistent with developmental modulation rather than immune activation. In contrast, S. strictum elicited a negligible transcriptional response, downregulating only a single pathway linked to diterpenoid biosynthesis. This silent interaction may reflect a commensal, latent, or stress-contingent role. Our findings highlight the plasticity of plant-endophyte communication and provide ecological insight into species-specific modes of interaction, with potential exploitation for sustainable agriculture. Understanding these subtle and species-specific responses offers a foundation for harnessing endogenous fungal microbiota in crop resilience strategies, particularly under climate-related stress scenarios.