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High-throughput analysis of transcriptome variation during water deficit in a poplar hybrid: a general overview

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Abstract

Poplar interspecific hybrids are one of the most important forest crops. In order to obtain data on molecular responses of forest trees to drought, Illumina sequencing technology was used to determine the sequence of most gene transcripts. This approach identified genes that contribute to tolerance to water-limiting environments, contributing to the long-term aim of developing strategies to improve plant productivity under drought. We generated 72,197,113 sequence reads, each 51 nt in length, encompassing 3.68 Gb of sequence from 12 cDNA libraries obtained from leaves of plants of a hybrid between Populus deltoides and Populus nigra subjected or not to moderate or severe drought. The expression of 41,335 poplar genes included in the Populus trichocarpa Phytozome database was studied by mapping Illumina cDNA reads on poplar unigene models. Expressed genes were characterised by gene ontology and by determining the metabolic pathway to which they belong. Most genes detected were expressed in control and drought-treated plants; however, a number of genes that were observed were significantly induced or repressed by drought. Induction or repression of most genes was more common after severe (relative water content around 55–60 %) than after moderate water deficit (around 85 %) even for genes that usually respond promptly to changes in environmental conditions, such as those encoding transcription factors. The dataset of expression profiles will be useful for future studies on responses to other stimula and for crop improvement of poplar.

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Acknowledgments

This research work was supported by PRIN-MIUR, Italy, project “Verso la delucidazione delle basi molecolari dell’eterosi nelle piante coltivate: variazione cis-regolatoria ed espressione genica in ibridi di pioppo”.

Thanks are due to Dr. Catherine Bastien (INRA-UAGPF, Orleans, France) for ensuring availability of the hybrid plants, to Dr. Michele Braidotti (Arizona Genomics Institute) for collaboration on data handling and treatment, and to Dr. John A. Walsh (Warwick University, UK) for critical reading of the manuscript.

Data archiving statement

All cDNA raw Illumina sequences used in this work are available at the NCBI Sequence Read Archive under the accession number SRP024267 (Submission: Populus x canadensis RNAseq).

The global analysis of gene expression is reported as an excel file, available at the Department of Agriculture, Food, and Environment of Pisa University repository website (http://www.agr.unipi.it/Sequence-Repository.358.0.html), in which each gene was represented by its absolute expression level in control, moderately dehydrated and severely dehydrated leaves.

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Correspondence to Lucia Natali.

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Communicated by D. Neale

Rosa Maria Cossu and Tommaso Giordani contributed equally to this work.

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Supplementary Material 1

Photographs of leaves of control and treated plants at two sampling stages (DOC 2205 kb)

Supplementary Material 2

Primers used for RT-PCR of 10 Populus trichocarpa selected genes (F: forward; R: reverse) (DOC 54 kb)

Supplementary Material 3

List of GO terms that are significantly (p < 0.05) enriched in genes that were up- or down-regulated in D1 or D2 compared to control, obtained using gProfiler software (XLS 119 kb)

Supplementary Material 4

GO terms, feature IDs, and annotations (when available) of genes activated or repressed during water deprivation, analysed at BLAST2GO website. For the sake of simplicity, only low level GO terms are reported (XLS 1139 kb)

Supplementary Material 5

Feature IDs, annotations and codes (as reported in Fig. 6) of genes involved in regulation of transcription, analysed using Mapman software (DOC 495 kb)

Supplementary Material 6

Feature IDs and annotations of genes involved in ABA-related drought response, or in ABA-independent signalling pathways, selected according to Cohen et al. (2010) (DOC 52 kb)

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Cossu, R.M., Giordani, T., Cavallini, A. et al. High-throughput analysis of transcriptome variation during water deficit in a poplar hybrid: a general overview. Tree Genetics & Genomes 10, 53–66 (2014). https://doi.org/10.1007/s11295-013-0661-5

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