Study : Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress

Identification

Name

Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress

Identifier

dXJuOkVWQS9zdHVkeS9QUkpOQTQxNDE3OA==

Source

Data link

Link to this study on EBI European Nucleotide Archive

Description

Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis suggested the enrichment of IAR genes involved in response to various stimuli or stresses. According to KEGG pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice. Overall design: Rice leaves mRNA profiles of physcion and chrysophanol alone treatment and combination treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

Data files

Genotype

Accession number	Name	Taxon