Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

Abstract

Background: The 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. Results: Using 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. Conclusion: Extensive, 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

Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat

“…These indicated that the identified genes could be the candidate genes for XZSN having higher drought resistance ability than LK3. In some plants, it was shown that the rapid and dramatic transcriptional reprogramming of the stress tolerance genotype contributes to higher stress resistance than the susceptible genotype ( Dossa et al., 2017 ; Simopoulos et al., 2020 ; Waititu et al., 2021 ; Yang et al., 2021 ). Interestingly, among these identified genes, over 90% of the genes were identified at drought treatment for 5 days, and over half of them in LK3 were not induced or inhibited at drought treatment for 5 days but were obviously upregulated or downregulated at drought treatment for 7 days ( Figure 6 ).…”

Global Warming, Climate Change, and Environmental Pollution: Recipe for a Multifactorial Stress Combination Disaster

“…A completely different approach could be to focus on pathways and genes that are unique to a multifactorial stress combination [31]. An additional strategy could be to identify and study plants that are subjected to extreme and multifactorial stress conditions in nature (e.g., desert plants, plants growing under harsh conditions in industrial waste sites, salt marshes, and/or next to hot springs, and/or some invasive species) [84][85][86], and…”

Multiple paths lead to salt tolerance - pre-adaptation vs dynamic responses from two closely related extremophytes

“…Molecular phenotypes for transcriptional preadaptation associated with multiple abiotic stresses have been reported for S. parvula and E. salsugineum separately to highlight genes uniformly expressed before and after stress treatments compared to differential expression of orthologs in a stress sensitive sister species (Gong et al, 2005;Oh et al, 2014;Lee et al, 2016;Simopoulos et al, 2020;Wang et al, 2021;Pantha et al, 2021). Our work indicated that stressassociated functional gene clusters that exhibit transcriptional preadaptation in one extremophyte is in many instances contrasted by a dynamic induced response by the orthologs from the other extremophyte that ultimately match the expression level found in the preadapted species (e.g.…”