Abstract
BackgroundArundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available.ResultsWe obtained by Illumina-based RNA-seq the whole root and shoot transcriptomes of young A. donax plants subjected to osmotic/water stress with 10 and 20 % polyethylene glycol (PEG; 3 biological replicates/organ/condition corresponding to 18 RNA-Seq libraries), and identified a total of 3034 differentially expressed genes. Blast-based mining of stress-related genes indicated the higher responsivity of roots compared to shoots at the early stages of water stress especially under the milder PEG treatment, with a majority of genes responsive to salt, oxidative, and dehydration stress. Analysis of gene ontology terms underlined the qualitatively different responses between root and shoot tissues. Among the most significantly enriched metabolic pathways identified using a Fisher’s exact test with FDR correction, a crucial role was played in both shoots and roots by genes involved in the signaling cascade of abscisic acid. We further identified relatively large organ-specific differences in the patterns of drought-related transcription factor AP2-EREBP, AUX/IAA, MYB, bZIP, C2H2, and GRAS families, which may underlie the transcriptional reprogramming differences between organs. Through comparative analyses with major Poaceae species based on Blast, we finally identified a set of 53 orthologs that can be considered as a core of evolutionary conserved genes important to mediate water stress responses in the family.ConclusionsThis study provides the first characterization of A. donax transcriptome in response to water stress, thus shedding novel light at the molecular level on the mechanisms of stress response and adaptation in this emerging bioenergy species. The inventory of early-responsive genes to water stress identified could constitute useful markers of the physiological status of A. donax and be a basis for the improvement of its productivity under water limitation. The full water-stressed A. donax transcriptome is available for Blast-based homology searches through a dedicated web server (http://ecogenomics.fmach.it/arundo/).Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0471-8) contains supplementary material, which is available to authorized users.
Highlights
Arundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available
If on one hand this resistance causes the high invasiveness of this plant, on the other hand it makes A. donax an excellent bioenergy crop, which can grow with very low management input even in marginal lands or in fields irrigated with waste or salty water [10]
Leveraging on the recent obtainment of the first reference transcriptome of A. donax by RNA sequencing (RNA-Seq) [24] and on the existing knowledge of the genetics of drought responses in plants, in this study we report the characterization of early transcriptional responses to two levels of polyethylene glycol (PEG)-induced water deficit in cohorts of young giant reed cuttings
Summary
Arundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available. Plant species dedicated to energy production (called bioenergy crops) are normally better biomass producers than food crops, resulting in higher ethanol yields per unit of cultivated area. A. donax, commonly called giant reed, is a perennial C3, polyploid, bamboo-like grass of the Poaceae family. It favors well-drained soils with abundant moisture, where it can form dense stands up to 6–10 m high with yields of up to 40 tons per hectare each year (comparable, or even exceeding, those of some C4 species) [4]. If on one hand this resistance causes the high invasiveness of this plant, on the other hand it makes A. donax an excellent bioenergy crop, which can grow with very low management input (e.g., pesticides, fertilization, irrigation) even in marginal lands or in fields irrigated with waste or salty water [10]
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