Abstract
BackgroundThe severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research.ResultsUsing comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for both ecotypes. We detected 1,007 long non-protein coding RNAs (lncRNAs), 8% were only expressed in stress-treated plants, a surprising outcome given the documented association between lncRNA expression and stress. Co-expression network analysis of the transcriptomes identified eight gene clusters where at least half of the genes in each cluster were differentially expressed. While many gene clusters were correlated to drought treatments, only a single cluster significantly correlated to drought exposure in both ecotypes.ConclusionExtensive, ecotype-specific transcriptional reprogramming with drought was unexpected given that both ecotypes are adapted to saline habitats providing persistent exposure to osmotic stress. This ecotype-specific response would have escaped notice had we used a single exposure to water deficit. Finally, the apparent capacity to improve tolerance and growth after a drought episode represents an important adaptive trait for a plant that thrives under semi-arid Yukon conditions, and may be similarly advantageous for crop species experiencing stresses attributed to climate change.
Highlights
The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population
RNA-Seq of E. salsugineum accessions following drought and recovery We analysed leaf transcriptomes of Yukon and Shandong Eutrema salsugineum plants subjected to a progressive, two-stage drought treatment protocol that considers the fraction of transpirable soil water (FTSW) at harvest as described by MacLeod et al (2015) [17]
Using principal component analysis (PCA), few differences were observed between the two sequencing time points by way of library overlap visualized in a PCA biplot (Additional file 1: Fig. S1)
Summary
The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. An improved understanding of how plants both respond to and recover from drought is vital to maintaining and improving crop yields to meet a growing world population, one forecast to reach 9 billion by 2050 [5]. Despite the growing need for crops that better manage water deficits, developing crops with improved drought tolerance has met with little success to date, in part because our basic knowledge of plant processes contributing to tolerance is poor and gene targets for crop improvement are, as yet, ill defined [6]
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