Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage

ABSTRACT: Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsHSFA2e loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Andy Pereira

PROVIDER: E-GEOD-65025 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Rice is susceptible to both heat and drought stress, in particular during flowering and grain filling, when both grain yield and quality may be severely compromised. However, under field conditions, these two stresses rarely occur separately. Under well-watered conditions, plants avoid heat stress by transpirational cooling, while this is not possible under drought conditions. Although investigating combined heat and drought stress is clearly more agronomically relevant than analyzing the effects of the single stresses, only a few studies of this stress combination, in particular under field conditions, have been published. Furthermore, little is known about how plants respond during recovery from drought stress, which also determines plant survival. To address these knowledge gaps, three rice cultivars differing in heat and drought tolerance were grown in the field under control and drought conditions in three consecutive years. Drought was applied either during flowering or during early grain filling, resulting in simultaneous heat stress, leading to reduced grain yield and quality. Analysis by gas chromatography-mass spectrometry (GC-MS) showed distinct metabolic profiles for the three investigated organs (flag leaves, flowering spikelets, developing seeds). The metabolic responses of the plants also strongly differed between cultivars and organs, and between stress and rewatering conditions. Correlation analysis identified potential metabolic markers for grain yield and quality under combined heat and drought stress from stress- and rewatering-regulated metabolites and from metabolites with constitutive differences between the cultivars. These results show that GC-MS can resolve metabolic responses to combined heat and drought stress and subsequent rewatering in different organs of field-grown rice. The metabolite profiles can be used to identify potential marker metabolites for yield stability and grain quality that are expected to improve breeding efforts towards climate change resilient rice.

Dataset Information

Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure