Transcriptomic Studies of Transgenic Manipulation of Ammonium Assimilation in Poplar: Mechanisms for Pleiotropic Phenotypes

Hybrid poplar (Populus tremula X P. alba, INRA 717-1-B4) engineered to express ectopically the pine cytosolic glutamine synthetase (GS1a) show distinct pleiotropic phenotypes, including enhanced nitrogen utilization efficiency, enhancements in plant growth, and enhanced tolerance to drought.  We have used the Agilent poplar whole genome array to characterize alterations in the transcriptome of GS poplars.  These studies allow identification of particular genes, gene networks, effectors, and markers for growth and drought tolerance that could be important in selecting specific genotypes.  Under well-watered conditions, a large number of genes showed differential expression in above-ground tissues of GS transgenics.  Among genes up-regulated in the GS transgenics were genes associated with protein turnover and stress responses, while many transcription factors were down-regulated.  Drought treatment attenuated the up-regulation response in above-ground tissues, but less so for down-regulated genes resulting in an increase in the presence of drought-significant groups up-regulated across all tissues.  Using Spearman correlation coefficients as the similarity measure, microarray data sets have been used to create preliminary GS and wild type networks.  The preliminary wild type network based on topological overlap matrix (TOM) has revealed 10 defined expression modules, whereas 13 expression modules were revealed in the GS network.  Considerable transcriptome rewiring was evident in the GS network with overall lower connectivity and fewer highly connected hubs than in the wild-type network.  A number of hub genes exhibited strikingly different connectivity between the two networks.  These results are consistent with phenotypic pleiotropy resulting from over-expression of a single gene in the central nitrogen assimilation pathway.