Biotic response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations

Extensive laboratory experimentation has revealed conserved molecular pathways controlling growth and stress responses in plants, yet how these programs operate in natural settings remains poorly understood. We have investigated the organization of the transcriptome in wild populations of Arabidopsis thaliana by sampling plants across 60 natural sites in Europe and North America over two seasons. Transcriptomes varied extensively among individuals and were only weakly structured by geography or season. No groups of plants stood out due to clear biotic or abiotic stress signatures known from the laboratory. While only a small portion of transcriptome variance was explained by disease symptoms or environmental and phenotypic variables, infection-associated signals accounted for the largest share of the explainable fraction. Biotic-response networks identified in controlled laboratory conditions were well conserved in wild transcriptomes, while other networks, including abiotic-response networks were substantially reorganized in wild plants. Together, these results indicate that while certain transcriptional modules are easily reidentified when moving from the wild to controlled conditions, many regulatory relationships differ in these two contexts, highlighting how ecological complexity shapes transcriptome organization in natural populations.