title: Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance.
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.
authors.affiliation: Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Kusunoki
authors.affiliation: Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Nakano
authors.affiliation: NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Sakata
authors.affiliation: Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Koyama
authors.affiliation: Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Kobayashi
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics*; D000535:Aluminum / Q000633:toxicity*; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000502:physiology*; D004269:DNA, Bacterial / Q000235:genetics; D060146:Ecotype; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D055786:Gene Knockout Techniques; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056726:Genetic Association Studies; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D059386:Reverse Genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; C036483:T-DNA; D000535:Aluminum
keywords: Arabidopsis; RNA-Seq; aluminium tolerance; expression-level polymorphism; natural variation; root; transcriptome