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Transcriptome differences between a transgenic poplar tolerant to drought and the control in different growth conditions

ABSTRACT: Transgenic hybrid poplars engineered to express ectopically the heterologous pine cytosolic GS1a display a number of significant pleiotropic phenotypes including enhanced growth, enhanced nitrogen use efficiency (NUE), and resistance to drought stress. The present study was undertaken in order to assess mechanisms whereby ectopic expression of pine GS1a in transgenic poplars results in enhanced agronomic phenotypes. Microarray analysis using the Agilent Populus whole genome array has allowed identification of genes differentially expressed between wild type and GS transgenics in four tissues (sink leaves, source leaves, stems, and roots) under three growth conditions (well-watered, drought, and recovery). Genes whose expression is significantly altered showing a minimum of 2‐fold differential expression between transgenic and wild type samples were selected for further analysis. Significantly over-represented functional categories among differentially-expressed genes have been identified. Two weighted co-expression networks were constructed analyzing separately GS transgenic and wild type transcript profile data. Differential network behavior and differential gene connectivities between GS and the wild type (WT) expression profiles have been analyzed. Transcript levels for some differentially expressed candidates were validated by q-PCR. The results show that ectopic expression of the pine GS1a in poplars results in transcriptomic rewiring affecting expression of genes belonging to relevant functional categories, including hormone metabolism, regulation of transcription, and stress related genes.

ORGANISM(S): Populus tremula x Populus alba Populus trichocarpa

PROVIDER: GSE59433 | GEO | 2016/12/30

SECONDARY ACCESSION(S): PRJNA255306

REPOSITORIES: GEO

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Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison

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Transcriptome differences between a transgenic poplar tolerant to drought and the control in different growth conditions

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