Sequence database of 1172 T-DNA insertion sites in Arabidopsis activation-tagging lines that showed phenotypes in T1 generation

Authors

  • Takanari Ichikawa,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1, Miki Nakazawa,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1, Mika Kawashima,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Shu Muto,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 2 Kazushi Gohda,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Kumiko Suzuki,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Akie Ishikawa,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Hiroko Kobayashi,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Takeshi Yoshizumi,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Yuko Tsumoto,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Yumi Tsuhara,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Haruko Iizumi,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • 1 Yukiko Goto,

    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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  • and 1 Minami Matsui 1,

    Corresponding author
    1. 1 Plant Function Exploration Team, Plant Functional Genomics Research Group, Genomic Sciences Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Kanagawa 230-0045, Japan, and2VALWAY Technology Center NEC Soft Ltd., 1-18-6 Shinkiba, Koto-ku, Tokyo 136-8608, Japan
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For correspondence (fax +81 45 503 9586; e-mail minami@postman.riken.go.jp).

These authors contributed equally to this study.

Summary

Plant genomic resources harbouring gain-of-function mutations remain rare, even though this type of mutation is believed to be one of the most useful for elucidating the function of unknown genes that have redundant partners in the genome. An activation-tagging T-DNA was introduced into the genome of Arabidopsis creating 55 431 independent transformed lines. Of these T1 lines, 1262 showed phenotypes different from those of wild-type plants. We called these lines ‘AT1Ps’ (activation T1 putants). The phenotypes observed include abnormalities in morphology, growth rate, plant colour, flowering time and fertility. Similar phenotypes re-appeared either in dominant or semi-dominant fashion in 17% of 177 AT2P plants tested. Plasmid rescue or an adaptor-PCR method was used to identify 1172 independent genomic loci of T-DNA integration sites in the AT1P plants. Mapping of the integration sites revealed that the chromosomal distribution of these sites is similar to that observed in conventional T-DNA knock-out lines, except that the intragenic type of integration is slightly lower (27%) in the AT1P plants compared to that observed in other random knock-out populations (30–35%). Ten AT2P lines that showed dominant phenotypes were chosen to monitor expression levels of genes adjacent to the T-DNA integration sites by RT-PCR. Activation was observed in 7 out of 17 of the adjacent genes detected. Genes located up to 8.2 kb away from the enhancer sequence were activated. One of the seven activated genes was located close to the left-border sequence of the T-DNA, having an estimated distance of 5.7 kb from the enhancer. Surprisingly, one gene, the first ATG of which is located 12 kb away from the enhancer, showed reduced mRNA accumulation in the tagged line. Application of the database generated to Arabidopsis functional genomics research is discussed. The sequence database of the 1172 loci from the AT1P plants is available (http://pfgweb.gsc.riken.go.jp/index.html).

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