Long-term transcriptional memory in rice plants submitted to salt shock
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ABSTRACT:
PROVIDER: PRJNA628609 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11614374_1.fastq.gz | Fastqsanger.gz | |||
| SRR11614374_2.fastq.gz | Fastqsanger.gz | |||
| SRR11614375_1.fastq.gz | Fastqsanger.gz | |||
| SRR11614375_2.fastq.gz | Fastqsanger.gz | |||
| SRR11614376_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Soil salinity is one of the main environmental factors that negatively influences yield, especially for sensitive crops such as rice. Studies report that a disturbing event can prepare the plant for a subsequent event through memory acquisition, involving physiological and molecular processes. Therefore, genes that provide altered responses in subsequent events define a category known as "memory genes." In this work, the RNA-Sequencing (RNA-Seq) technique was used to analyse the transcriptional profile of rice plants subjected to different salt shock events and to characterise genes associated with long-term memory. Methods: The mRNA of rice plants cv. Ligeirinho was generated using deep sequencing, in duplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (SV), plants were exposed to saline shock only at the vegetative stage; III) reproductive (SR) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (SV+R), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event). The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays. Results: Plants subjected to recurrent salt shock showed differences in differentially expressed genes (DEGs). Additionally, the mammalian target of rapamycin (mTOR) pathways, and carbohydrate and amino acid associated pathways were altered under all conditions. Memory genes can be classified according to their responses during the first event (+ or –) and the second shock event (+ or –), being possible to observe a larger number of transcripts for groups [+/–] and [–/+], genes characterised as "revised response." Conclusions: This is the first long-term transcriptional memory study in rice plants under salt shock, providing new insights into the process of plant memory acquisition.
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Project description:We used a custom-designed microarray to characterize the transcriptional response that accompanies longt-term sensitization training in the marine mollusk Aplysia californica. We characterized transcription for a new memory (1 day after training), a forgotten memory (8 days after training) and for a long-term savings memory (8 days after training but 1 day after a reminder that re-instates the sensitization memory). All animals received a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock). This produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training). In the forgetting condition, animals received training on day 1, and post-tests on days 7 and 8 showed little-to-no evidence of recall (T-SWR responses on the trained side returned to close to baseline). In the savings condition, animals received training on day 1 that produced strong sensitization, showed forgetting on day 7, and then received a weak bilateral shock as a reminder (day 7), producing a long-term savings memory on day 8 (a re-instatement of the behavioral expression of sensitization on the previously trained side). In the new memory condition, animals received sham training on day 1, then real training on day 7, producing robust sensitization measured on day 8. Pleural ganglia were harvested on day 8. Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression. The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.
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Project description:In this study, we have analyzed the expression profiles of rice genes under control and heat shock conditions using microarray technology to identify the genes differentially expressed. Experiment Overall Design: 14-day-old light-grown rice seedlings grown under controlled conditions and those subjected to heat shock were used for RNA extraction and hybridization on Affymetrix microarrays. Three technical replicates of each sample were used for microarray analysis. For heat shock treatment, the seedlings were kept in a chamber at 42 degree C. The seedlings kept at 28-30 degree C, served as control (Seedling).
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