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Frequency and character of alternative somatic recombination fates of paralogous genes during T-DNA integration

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Abstract

A synthetic RBCSB gene cluster was transformed into Arabidopsis in order to simultaneously evaluate the frequency and character of somatic illegitimate recombination, homologous recombination, and targeted gene replacement events associated with T-DNA-mediated transformation. The most frequent type of recombination event observed was illegitimate integration of the T-DNA without activation of the silent ΔRBCS1B: LUC transgene. Sixteen luc+ (firefly luciferase positive) T1 plants were isolated. Six of these were due to illegitimate recombination events resulting in a gene trapping effect. Nine resulted from homologous recombination between paralogous RBCSB sequences associated with T-DNA integration. The frequency of somatic homologous recombination associated with T-DNA integration was almost 200 times higher than previously reported rates of meiotic homologous recombination with the same genes. The distribution of (somatic homologous) recombination resolution sites generally fits a fractional interval length model. However, a small region adjacent to an indel showed a significant over-representation of resolution sites, suggesting that DNA mismatch recognition may also play an important role in the positioning of somatic resolution sites. The frequency of somatic resolution within exon-2 was significantly different from that previously observed during meiotic recombination.

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Acknowledgements

We are grateful to our colleagues who helped to make this experiment possible: Michael Timko for providing pATS5 and pATS17, Masaki Furuya for the generous use of his single photon video imaging equipment during the isolation of T1 luc+ seedlings, Kenko Uchida, Norihito Kuno, and Tomoko Shinomura for orienting J.G.J in technical and personal matters during his visit to the Furuya laboratory, Keying Ye for statistical consulting, and John M. McDowell for critical review of the manuscript. This work was supported by grants from the Monsanto Company and the National Science Foundation (IBN9727044) to WG while he was at UC Berkeley. JGJ was supported by a National Science Foundation Postdoctoral Fellowship in Plant Biology (BIR9404014), a NSF Center for Global Partnership (INT-9622319), and a National Institutes of Health grant (R01GM62352). We are also grateful for the helpful comments by the anonymous reviewers.

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  1. Kristy Carter

    Present address: PPDI, 2244 Dabney Road, Richmond, VA, 23230-3323, USA

  2. Yuki Kinoshita

    Present address: National Institute of Genetics, Agricultural Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan

  3. Wilhelm Gruissem

    Present address: Institute of Plant Sciences, Swiss Federal Institute of Technology, ETH Zentrum, LFW E57.1, 8092, Zurich, Switzerland

Authors and Affiliations

  1. Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA

    John G. Jelesko, Yuki Kinoshita & Wilhelm Gruissem

  2. Department of Plant Pathology, Physiology, and Weed Science, Fralin Biotechnology Center, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061-0346, USA

    Kristy Carter

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Correspondence to John G. Jelesko.

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Communicated by M.-A. Grandbastien

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Jelesko, J.G., Carter, K., Kinoshita, Y. et al. Frequency and character of alternative somatic recombination fates of paralogous genes during T-DNA integration. Mol Genet Genomics 274, 91–102 (2005). https://doi.org/10.1007/s00438-005-0001-z

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