Genotypic and tissue-specific variation of Populus nigra transcriptome profiles in response to drought

Abstract

Climate change is one of the most important challenges for mankind in the far and near future. In this regard, sustainable production of woody crops on marginal land with low water availability is a major challenge to tackle. This dataset is part of an experiment, in which we exposed three genetically differentiated genotypes of Populus nigra originating from contrasting natural habitats to gradually increasing moderate drought. RNA sequencing was performed on fine roots, developing xylem and leaves of those three genotypes under control and moderate drought conditions in order to get a comprehensive dataset on the transcriptional changes at the whole plant level under water limiting conditions. This dataset has already provided insight in the transcriptional control of saccharification potential of the three Populus genotypes under drought conditions and we suggest that our data will be valuable for further in-depth analysis regarding candidate gene identification or, on a bigger scale, for meta-transcriptome analysis.

Fig. 1

Experimental setup and data processing pipeline. (a) Water availability was reduced for two weeks to reach 20% soil extractable water (SEW) and was kept constant for 3 more weeks until harvest. (b) Flow chart of RNA sample processing from harvest to data analysis.

Fig. 2

Quality assessment of RNA sequencing data. (a) Mean quality phred scores of individual samples, (b) Per Sequence Quality Scores as counts per phred score (c) GC content of individual samples. FastQC results for single samples were summarized using MulitQC.

Fig. 3

Initial analysis of RNAseq data from control- or drought-stress samples of fine roots, developing xylem and leaf samples of three genotypes of P. nigra originating from Spain, France and Italy. (a–d) Principal component analyses of VST normalized RNA-seq count data (a) PCA of all tissues and ecotypes; (b) PCA of leaf samples; (c) PCA of developing xylem samples; (d) PCA of fine root samples; (e) Venn diagram showing the distribution of DEGs under drought between the three tissues regardless of the genotype. (f–h) Venn diagrams showing the intersections of drought-regulated DEGs between the genotypes for fine roots (f), developing xylem (g) and leaf (h).