A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system

Hidemitsu Nakamura, Makoto Hakata, Kou Amano, Akio Miyao, Naoko Toki, Mariko Kajikawa, Jinhuan Pang, Naokuni Higashi, Shigeko Ando, Seiichi Toki, Miki Fujita, Akiko Enju, Motoaki Seki, Miki Nakazawa, Takanari Ichikawa, Kazuo Shinozaki, Minami Matsui, Yoshiaki Nagamura, Hirohiko Hirochika, Hiroaki Ichikawa

Research output: Contribution to journalArticlepeer-review

83 Citations (Scopus)
1 Downloads (Pure)


The latest report has estimated the number of rice genes to be ∼32 000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13 980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12 000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene, confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.

Original languageEnglish
Pages (from-to)357-371
Number of pages15
JournalPlant Molecular Biology
Issue number4
Publication statusPublished - Nov 2007
Externally publishedYes


  • Full-length cDNA
  • Functional genomics
  • Gain-of-function
  • Oryza sativa
  • Rice
  • Transgenic plants

Field of Science*

  • 1.6 Biological sciences
  • 4.1 Agriculture, Forestry, and Fisheries

Publication Type*

  • 1.1. Scientific article indexed in Web of Science and/or Scopus database


Dive into the research topics of 'A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system'. Together they form a unique fingerprint.

Cite this