Effect of Endophytic Inoculation on the Wheat Transcriptome

Fungal endophytes are increasingly recognised as key modulators of plant physiology, yet their molecular impact on major crops such as wheat (Triticum aestivum L.) remains underexplored. Here, we investigated the transcriptomic responses of wheat (Triticum aestivum L.) to four endophytic fungi-Penicillium olsonii, Chrysosporium pseudomerdarium, Sarocladium spinificis, and Sarocladium strictum-previously isolated from the wheat endosphere. Using high-resolution RNA-seq, we reveal that each fungus elicits a distinct transcriptional landscape in wheat seedlings, reflecting divergent modes of host interaction.P. 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. S. 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.This study provides the first comprehensive transcriptomic comparison of wheat responses to multiple native endophytes and uncovers a functional continuum ranging from active transcriptional modulation to latent colonisation. Our findings highlight the plasticity of plant-endophyte communication and its 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.