A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis

Takashi Kuromori, Takuji Wada, Asako Kamiya, Masahiro Yuguchi, Takuro Yokouchi, Yuko Imura, Hiroko Takabe, Tetsuya Sakurai, Kenji Akiyama, Takashi Hirayama, Kiyotaka Okada, Kazuo Shinozaki

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Mutant lines covering all Arabidopsis genes allow us to pursue systematic functional genomics. A comprehensive phenotype description, called a phenome, is highly sought after in the profiling of -omics data. We selected 4000 transposon-insertional lines with transposon insertions in their gene-coding regions, and systematically observed the visible phenotype of each line. For the first 3 weeks after germination, plants were grown on agar plates and the juvenile phenotypes were recorded. Then the plants were transferred to soil and their phenotypes were recorded at each growth stage. About 140 lines showed clear and reproducible visible phenotypes, including novel phenotypic mutants as well as previously reported ones. All descriptions of the mutants showing visible phenotypes were classified into eight primary categories (seedling, leaves, flowering and growth, stems, branching, flowers, siliques and seed yield) and 43 secondary categories of morphological phenotypes. Phenotypic images have been entered into a searchable database (http:// rarge.gsc.riken.jp/phenome/). One example investigated through the use of plural alleles was a mutant of a novel gene related to glycerolipid biosynthesis, with a unique visible phenotype of sepal opening. Our results suggest that we can find more novel visible phenotypes and their corresponding genes, and that phenotypic mutants of gene knockouts are not exhausted yet. This study provides basic data on large-scale phenotyping of gene knockout lines in plants, and will contribute to the completion of an international effort to develop a phenome database of all the functional genes in Arabidopsis.

Original languageEnglish
Pages (from-to)640-651
Number of pages12
JournalPlant Journal
Volume47
Issue number4
DOIs
Publication statusPublished - Aug 2006
Externally publishedYes

Fingerprint

Arabidopsis
Phenotype
phenotype
mutants
Genes
genes
Gene Knockout Techniques
gene targeting
transposons
Databases
Growth
Germination
Genomics
Seedlings
stem elongation
calyx
Agar
Seeds
seed yield
Soil

Keywords

  • Arabidopsis thaliana
  • Gene knockout
  • Phenotyping
  • Transposon
  • Visible phenotype

ASJC Scopus subject areas

  • Plant Science

Cite this

Kuromori, T., Wada, T., Kamiya, A., Yuguchi, M., Yokouchi, T., Imura, Y., ... Shinozaki, K. (2006). A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. Plant Journal, 47(4), 640-651. https://doi.org/10.1111/j.1365-313X.2006.02808.x

A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. / Kuromori, Takashi; Wada, Takuji; Kamiya, Asako; Yuguchi, Masahiro; Yokouchi, Takuro; Imura, Yuko; Takabe, Hiroko; Sakurai, Tetsuya; Akiyama, Kenji; Hirayama, Takashi; Okada, Kiyotaka; Shinozaki, Kazuo.

In: Plant Journal, Vol. 47, No. 4, 08.2006, p. 640-651.

Research output: Contribution to journalArticle

Kuromori, T, Wada, T, Kamiya, A, Yuguchi, M, Yokouchi, T, Imura, Y, Takabe, H, Sakurai, T, Akiyama, K, Hirayama, T, Okada, K & Shinozaki, K 2006, 'A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis', Plant Journal, vol. 47, no. 4, pp. 640-651. https://doi.org/10.1111/j.1365-313X.2006.02808.x
Kuromori, Takashi ; Wada, Takuji ; Kamiya, Asako ; Yuguchi, Masahiro ; Yokouchi, Takuro ; Imura, Yuko ; Takabe, Hiroko ; Sakurai, Tetsuya ; Akiyama, Kenji ; Hirayama, Takashi ; Okada, Kiyotaka ; Shinozaki, Kazuo. / A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis. In: Plant Journal. 2006 ; Vol. 47, No. 4. pp. 640-651.
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