Rootstock-dependent scion effects shape root transcriptomes in grafted Pinus pinaster
Maritime pine ( Pinus pinaster Aiton) is a key conifer in southwestern Europe showing ecological plasticity and economic importance. Understanding molecular interactions between above- and below-ground organs is essential for improving forest resilience and management under changing environmental conditions. Previous transcriptomic analyses of a full-sib family using progenitors from contrasting precipitation regions identified differences between drought-tolerant and drought-sensitive genotypes. Grafting experiments further indicated that rootstocks can modulate transcriptomes in aerial tissues. Here, we analyse truTranscriptomes were influenced by scion origin in a rootstock-dependent manner. In tolerant rootstocks, scions from an arid-region promoted transcriptional patterns related to resource conservation and root remodelling. Scions from a wetter region triggered transcriptional patterns related to broader metabolic adjustments. Sensitive rootstocks showed greater transcriptional responsiveness to scion identity, particularly in pathways related to primary metabolism, osmolyte synthesis and growth. A shared set of genes was consistently regulated across graft combinations, suggesting conserved components of scion–root communication. These findings provide the first comprehensive description of root transcriptomic variation in grafted maritime pine and advance a whole-plant framework for understanding molecular integration in conifers.