Transcriptome analysis reveals regulatory framework for salt and osmotic tolerance in a succulent xerophyte

Abstract

Background Zygophyllum xanthoxylum is a succulent xerophyte with remarkable tolerance to diverse abiotic stresses. Previous studies have revealed important physiological mechanisms and identified functional genes associated with stress tolerance. However, knowledge of the regulatory genes conferring stress tolerance in this species is poorly understood. Results Here, we present a comprehensive analysis of regulatory genes based on the transcriptome of Z. xanthoxylum roots exposed to osmotic stress and salt treatments. Significant changes were observed in transcripts related to known and obscure stress-related hormone signaling pathways, in particular abscisic acid and auxin. Significant changes were also found among key classes of early response regulatory genes encoding protein kinases, transcription factors, and ubiquitin-mediated proteolysis machinery. Network analysis shows a highly integrated matrix formed by these conserved and novel gene products associated with osmotic stress and salt in Z. xanthoxylum . Among them, two previously uncharacterized NAC (NAM/ATAF/CUC) transcription factor genes, ZxNAC083 (Unigene16368_All) and ZxNAC035 (CL6534.Contig1_All), conferred tolerance to salt and drought stress when constitutively overexpressed in Arabidopsis plants. Conclusions This study provides a unique framework for understanding osmotic stress and salt adaptation in Z. xanthoxylum including novel gene targets for engineering stress tolerance in susceptible crop species. Electronic supplementary material The online version of this article (10.1186/s12870-019-1686-1) contains supplementary material, which is available to authorized users.

Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

“…RNA sequencing (RNA-Seq) is a rapid and cost-effective method for both mapping and quantifying the transcriptome in eukaryotes and is widely used to analyze the gene expression in plants under specific developmental stages or physiological conditions, providing substantial insights into the molecular processes involved in plants' response to abiotic stresses [9,22]. In the present work, we generated a transcriptomic dataset for studying the molecular mechanisms of salt tolerance in P.…”

“…cycle, glutathione peroxidase (GPX) pathway, catalase (CAT) pathway and peroxiredoxin/thioredoxin (PrxR/Trx) pathway [9]. After salt treatment for 6 and 24 h, a total of 19 and 15 DEGs categorized in the abovementioned ROS-scavenging pathways in roots of P. cornutum were respectively upregulated and 5 and 29 DEGs were respectively downregulated ( Fig.…”

“…The breeding of crops with higher yield and quality under saline conditions by using molecular genetics is an effective strategy to promote food security [3,7,8]. Despite abundant molecular knowledge have derived from model plants such as Arabidopsis thaliana and Oryza sativa, a low capacity for stress tolerance limits their usefulness in current breeding programs [9]. Certain wild plant species, including halophytes and xerophytes, however, have evolved multiple protective mechanisms to successfully thrive in extremely harsh environments and, as a result, harbor prominent abiotic stress tolerance genes [10,11].…”

“…Transcription factors (TFs) are important and abundant regulatory genes in higher plants. The major classes of TFs include NAC (NAM/ATAF/CUC), AP2/ERF (APETALA2 and ethylene-responsive element binding proteins), bHLH (basic helix-loop-helix), MYB (myeloblastosis), WRKY (WRKY-domain), bZIP/HD-ZIP (basic region-leucine zipper/homeodomain-leucine zipper), ZF (zinc finger) and HSP (heat shock protein), some of which have been validated to confer salt and drought tolerance in various plant species by transcriptional regulation of downstream target stress-responsive genes[9]. As TFs generally show rapid responses to abiotic stresses, we only analyzed the differentially expressed TF genes in roots and shoots after 6 h of salt treatment (the number of the differentially expressed TF genes after salt treatment for 24 h was much lower than that after salt treatment for 6 h in our results; data not shown).…”

Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

“…The breeding of crops with higher yield and quality under saline conditions by using molecular genetics is an effective strategy to promote food security [3,7,8]. Despite abundant molecular knowledge have derived from model plantssuch as Arabidopsis thaliana and Oryza sativa, a low capacity for stress tolerance limits their usefulness in current breeding programs [9]. Certain wild plant species, including halophytes and xerophytes, however, have evolved multiple protective mechanisms to successfully thrive in extremely harsh environments and, as a result, harbor prominent abiotic stress tolerance genes [10,11].…”