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Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an salt shock

ABSTRACT: Expression profiling of a total of 7281 transcripts was compared between control and salt shock conditions.

ORGANISM(S): Mesorhizobium japonicum MAFF 303099

PROVIDER: GSE43530 | GEO | 2016/12/31

SECONDARY ACCESSION(S): PRJNA186728

REPOSITORIES: GEO

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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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Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an salt shock

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