Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance. (4th January 2017)

• Record Type: Journal Article
• Authors: Kusunoki, Kazutaka; Nakano, Yuki; Tanaka, Keisuke; Sakata, Yoichi; Koyama, Hiroyuki; Kobayashi, Yuriko
• Is Part Of: Plant, cell and environment. Volume 40:Number 2(2017)
• Page Start: 249
• Page End: 263
• Publication Date: 2017-01-04
• Subjects: Arabidopsis -- aluminium tolerance -- expression‐level polymorphism -- natural variation -- RNA‐Seq -- root -- transcriptome; Plant physiology -- Periodicals; Plant cells and tissues -- Periodicals; Plant communities -- Periodicals; 581.105
• DOI: 10.1111/pce.12866
• Languages: English
• ISSNs: 0140-7791

Abstract

Abstract: Differences in the expression levels of aluminium (Al) tolerance genes are a known determinant of Al tolerance among plant varieties. We combined transcriptomic analysis of six Arabidopsis thaliana accessions with contrasting Al tolerance and a reverse genetic approach to identify Al‐tolerance genes responsible for differences in Al tolerance between accession groups. Gene expression variation increased in the signal transduction process under Al stress and in growth‐related processes in the absence of stress. Co‐expression analysis and promoter single nucleotide polymorphism searching suggested that both trans ‐acting polymorphisms of Al signal transduction pathway and cis ‐acting polymorphisms in the promoter sequences caused the variations in gene expression associated with Al tolerance. Compared with the wild type, Al sensitivity increased in T‐DNA knockout (KO) lines for five genes, including TARGET OF AVRB OPERATION1 ( TAO1 ) and an unannotated gene ( At5g22530 ). These were identified from 53 Al‐inducible genes showing significantly higher expression in tolerant accessions than in sensitive accessions. These results indicate that the difference in transcriptional signalling is partly associated with the natural variation in Al tolerance in Arabidopsis . Our study also demonstrates the feasibility of comparative transcriptome analysis by using natural genetic variation for the identification of genes responsible for Al stress tolerance. Abstract : Aluminium (Al) tolerance is one of the most important agronomic traits for the production of crops in the acid soil regions around the world. Comparative transcriptome analyses using the six Arabidopsis accessions contrasting Al tolerance identified the relationship between expression level polymorphism (ELP) and Al tolerance. Five Al‐tolerance genes were newly identified from the gene set with ELP associated with Al tolerance. Differential pattern of the enrichment of promoter single nucleotide polymorphisms of the genes with ELP suggested that cis ‐regulatory and trans ‐regulatory mechanisms are involved in the ELP under Al stress.