Transcriptomic changes during senescence of leaves and fine roots of Populus trichocarpa

We studied the changes that occur in gene transcription during seasonal senescence in Populus trichocarpa pioneer leaves and fine roots. Plant senescence is a strictly regulated physiological process that allows relocating of valuable nutrients from senescent tissues before death. It might be induced by internal or external factors and among them, phytohormones play an undoubtedly significant role. Senescence was extensively studied in leaves, but the aging of other ephemeral organs, located underground, and its drivers are still poorly understood. We focused on collective results to fill in the knowledge gap about senescence of fine, absorptive roots and leaves in order to check if there are universal mechanisms involved during plant organ senescence. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in developmental PCD. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves decreased by approximately 65% and fine roots were dark brown or black color. Our results reveal the important role of phytohormones in regulating the senescence of both studied organs. The transcriptomic analyses showed significant changes in gene expression that are associated with phytohormones, especially with ABA and jasmonates. We conclude that phytohormonal regulation of senescence in roots and leaves is organ-specific. In roots, phytohormones are involved indirectly in regulation of senescence by increasing tolerance for cold or resistance for pathogens, whereas such correlation was not observed in leaves. All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray) growing in rhizotrons filled with natural soil with shoots extending from the top into the air. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves (LC) and the root (RC) system were fully developed and functional. The second group of leaf (LS1) and root (RS1) samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves (LS2) decreased by approximately 65% and fine roots (RS2) were dark brown or black color. Total RNA was extracted from three biological replicates of each stage of senescence of fine roots and leaves using an RNeasy Plant Mini kit (Qiagen, USA). RNA quantity and quality were assessed using a NanoDrop1000 (Thermo Fisher Scientific Inc., USA). cRNA synthesis and microarray hybridization to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) were performed according to the provided Affymetrix protocol.