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

doi:10.1007/s11103-007-9243-y

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 journal › Article › peer-review

92 Citations (Scopus)

13 Downloads (Pure)

Abstract

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 language	English
Pages (from-to)	357-371
Number of pages	15
Journal	Plant Molecular Biology
Volume	65
Issue number	4
DOIs	https://doi.org/10.1007/s11103-007-9243-y
Publication status	Published - Nov 2007
Externally published	Yes

Keywords*

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

Access to Document

10.1007/s11103-007-9243-y

A genome-wide gain-of-function analysis of rice genesFinal published version, 547 KB

Cite this

Nakamura, H., Hakata, M., Amano, K., Miyao, A., Toki, N., Kajikawa, M., Pang, J., Higashi, N., Ando, S., Toki, S., Fujita, M., Enju, A., Seki, M., Nakazawa, M., Ichikawa, T., Shinozaki, K., Matsui, M., Nagamura, Y., Hirochika, H., & Ichikawa, H. (2007). A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system. Plant Molecular Biology, 65(4), 357-371. https://doi.org/10.1007/s11103-007-9243-y

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title = "A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system",

abstract = "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.",

keywords = "Full-length cDNA, Functional genomics, Gain-of-function, Oryza sativa, Rice, Transgenic plants",

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

note = "Funding Information: Acknowledgements This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Green Technology Project EF-1004). We are grateful to Dr. Takuji Sasaki for his encouragement throughout the project and his excellent advice on the improvement of this manuscript, and to Dr. Shoshi Kikuchi for providing useful information on rice FL-cDNAs. We thank Professors Kokichi Hinata, Atsushi Hirai, Hiroshi Kamada and Masashi Ugaki for their encouragement, critical comments and helpful suggestions, and Drs. Hisato Okuizumi and Hiroyuki Kawahigashi for their administrative support throughout the project. We also thank Mayumi Akagawa, Hiroko Abe, Keiko Mori, Etsuko Sugai, Yumiko Nakane, Ken-ichi Watanabe, Mayumi Takeya, and Kana Miyata for their technical assistance; the members of the Technical Support Section of the National Institute of Agrobiological Sciences for their help in the care of the FOX-rice plants; Haruko Onodera and Kazuko Ono for their technical assistance and advice on rice transformation; Inplanta Innovations Inc. for their technical help on the construction of the",

year = "2007",

month = nov,

doi = "10.1007/s11103-007-9243-y",

language = "English",

volume = "65",

pages = "357--371",

journal = "Plant Molecular Biology",

issn = "0167-4412",

publisher = "Springer Science and Business Media B.V.",

number = "4",

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Nakamura, H, Hakata, M, Amano, K, Miyao, A, Toki, N, Kajikawa, M, Pang, J, Higashi, N, Ando, S, Toki, S, Fujita, M, Enju, A, Seki, M, Nakazawa, M, Ichikawa, T, Shinozaki, K, Matsui, M, Nagamura, Y, Hirochika, H & Ichikawa, H 2007, 'A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system', Plant Molecular Biology, vol. 65, no. 4, pp. 357-371. https://doi.org/10.1007/s11103-007-9243-y

TY - JOUR

T1 - A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system

AU - Nakamura, Hidemitsu

AU - Hakata, Makoto

AU - Amano, Kou

AU - Miyao, Akio

AU - Toki, Naoko

AU - Kajikawa, Mariko

AU - Pang, Jinhuan

AU - Higashi, Naokuni

AU - Ando, Shigeko

AU - Toki, Seiichi

AU - Fujita, Miki

AU - Enju, Akiko

AU - Seki, Motoaki

AU - Nakazawa, Miki

AU - Ichikawa, Takanari

AU - Shinozaki, Kazuo

AU - Matsui, Minami

AU - Nagamura, Yoshiaki

AU - Hirochika, Hirohiko

AU - Ichikawa, Hiroaki

N1 - Funding Information: Acknowledgements This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Green Technology Project EF-1004). We are grateful to Dr. Takuji Sasaki for his encouragement throughout the project and his excellent advice on the improvement of this manuscript, and to Dr. Shoshi Kikuchi for providing useful information on rice FL-cDNAs. We thank Professors Kokichi Hinata, Atsushi Hirai, Hiroshi Kamada and Masashi Ugaki for their encouragement, critical comments and helpful suggestions, and Drs. Hisato Okuizumi and Hiroyuki Kawahigashi for their administrative support throughout the project. We also thank Mayumi Akagawa, Hiroko Abe, Keiko Mori, Etsuko Sugai, Yumiko Nakane, Ken-ichi Watanabe, Mayumi Takeya, and Kana Miyata for their technical assistance; the members of the Technical Support Section of the National Institute of Agrobiological Sciences for their help in the care of the FOX-rice plants; Haruko Onodera and Kazuko Ono for their technical assistance and advice on rice transformation; Inplanta Innovations Inc. for their technical help on the construction of the

PY - 2007/11

Y1 - 2007/11

N2 - 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.

AB - 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.

KW - Full-length cDNA

KW - Functional genomics

KW - Gain-of-function

KW - Oryza sativa

KW - Rice

KW - Transgenic plants

UR - https://www.scopus.com/pages/publications/35348934989

U2 - 10.1007/s11103-007-9243-y

DO - 10.1007/s11103-007-9243-y

M3 - Article

C2 - 17929174

AN - SCOPUS:35348934989

SN - 0167-4412

VL - 65

SP - 357

EP - 371

JO - Plant Molecular Biology

JF - Plant Molecular Biology

IS - 4

ER -

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

Abstract

Keywords*

Field of Science*

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