Dataset Information

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

ABSTRACT: Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted plant cultivars. The aim of the present study was to investigate phenotypic and transcriptional drought responses in two willow genotypes (520 and 592) originating from an experimental cross between S. viminalis × (S. viminalis × S. schwerinii). Willows are woody perennials in the Salicaceae plant family that are grown as bioenergy crops worldwide.An experiment was conducted where plants were exposed to drought and different eco-physiological parameters were assessed. RNA-seq data was furthermore generated with the Illumina technology from root tips and leaves from plants grown in drought and well-watered (WW) conditions. The RNA-seq data was assembled de novo with the Trinity assembler to create a reference gene set to which the reads were mapped in order to obtain differentially expressed genes (DEGs) between the drought and WW conditions. To investigate molecular mechanisms involved in the drought response, GO enrichment analyses were conducted. Candidate genes with a putative function in the drought response were also identified.A total of 52,599 gene models were obtained and after filtering on gene expression (FPKM ? 1), 35,733 gene models remained, of which 24,421 contained open reading frames. A total of 5,112 unique DEGs were identified between drought and WW conditions, of which the majority were found in the root tips. Phenotypically, genotype 592 displayed less growth reduction in response to drought compared to genotype 520. At the transcriptional level, genotype 520 displayed a greater response in the leaves as more DEGs were found in genotype 520 compared to genotype 592. In contrast, the transcriptional responses in the root tips were rather similar between the two genotypes. A core set of candidate genes encoding proteins with a putative function in drought response was identified, for example MYBs and bZIPs as well as chlorophyll a/b binding proteins.We found substantial differences in drought responses between the genotypes, both at the phenotypic and transcriptional levels. In addition to the genotypic variation in several traits, we also found indications for genotypic variation in trait plasticity, which could play a role in drought adaptation. Furthermore, the two genotypes displayed overall similar transcriptional responses in the root tips, but more variation in the leaves. It is thus possible that the observed phenotypic differences could be a result of transcriptional differences mostly at the leaf level.This study has contributed to a better general understanding of drought responses in woody plants, specifically in willows, and has implications for breeding research towards more drought adapted plants.

SUBMITTER: Pucholt P

PROVIDER: S-EPMC4604075 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Pucholt Pascal P Sjödin Per P Weih Martin M Rönnberg-Wästljung Ann Christin AC Berlin Sofia S

BMC plant biology 20151012

<h4>Background</h4>Drought is a major environmental stress that can have severe impacts on plant productivity and survival. Understanding molecular mechanisms of drought responses is crucial in order to breed for drought adapted plant cultivars. The aim of the present study was to investigate phenotypic and transcriptional drought responses in two willow genotypes (520 and 592) originating from an experimental cross between S. viminalis × (S. viminalis × S. schwerinii). Willows are woody perenni ...[more]

PMID: 26458893

Similar Datasets

Project description:Quinoa is an important economic food crop. However, quinoa seedlings are susceptible to drought stress, and the molecular mechanism of drought tolerance remains unclear. In this study, we compared transcriptomic and physiological analyses of drought-tolerant (L1) and susceptible (HZ1) genotypes exposed to 20% PEG for 3 and 9 days at seedling stage. Compared with HZ1, drought stress had less damage to photosynthetic system, and the contents of SOD, POD and CAT were higher and the contents of H2O2 and O2 -were lower in L1 leaves. Based on the RNA-seq method, we identified 2423, 11856, 1138 and 3903 (HZ1-C3-VS-T3, HZ1-C9-vs-T9, L1-C3-vs-T3 and L1-C9-vs-T9) annotated DEGs. Go enrichment was shown in terms of Biological Process: DEGs involved in biological processes such as metabolic process, cellular process, and single-organism process were most abundant in all four comparison treatments. In Molecular Function: the molecular functions of catalytic activity, binding and transporter activity have the most DEGs in all four processes. Cellular Component: membrane, membrane part, and cell have the most DEGs in each of the four processes. These DEGs include AP2/ERF, MYB, bHLH, b-ZIP, WRKY, HD-ZIP, NAC, C3h and MADS, which encode transcription factors. In addition, the MAPK pathway, starch and sucrose metabolism, phenylpropanoid biosynthesis and plant hormone signal transduction were significantly induced under drought stress, among them, G-hydrolases-66, G-hydrolases-81, G-hydrolases-78, Su-synthase-02, Su-synthase-04, Su-synthase-06, BRI1-20 and bHLH17 were all downregulated at two drought stress points in two genotypes, PP2C01, PP2C03, PP2C05-PP2C07, PP2C10, F-box01 and F-box02 were upregulated at two drought stress points in two genotypes. These results agree with the physiological responses and RNA-seq results. Collectively, these findings may lead to a better understanding of drought tolerance, and some of the important DEGs detected in this study could be targeted for future research. And our results will provide a comprehensive basis for the molecular network that mediates drought tolerance in quinoa seedlings and promote the breeding of drought-resistant quinoa varieties.

Project description:To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum), physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control), 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA) level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs) (corresponding to 87 and 80 unique proteins, respectively) in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism was down-regulated in the roots, but enhanced in the leaves. These results will contribute to the existing knowledge on the complexity of root and leaf protein changes that occur in response to drought, and also provide a framework for further functional studies on the identified proteins.

Project description:BACKGROUND:Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species. RESULTS:Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought. CONCLUSIONS:In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.

Dataset Information

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Publications

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets