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Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis gene

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Abstract

The Lotus japonicus LjSYM2 gene, and the Pisum sativum orthologue PsSYM19, are required for the formation of nitrogen-fixing root nodules and arbuscular mycorrhiza. Here we describe the map-based cloning procedure leading to the isolation of both genes. Marker information from a classical AFLP marker-screen in Lotus was integrated with a comparative genomics approach, utilizing Arabidopsis genome sequence information and the pea genetic map. A network of gene-based markers linked in all three species was identified, suggesting local colinearity in the region around LjSYM2/PsSYM19. The closest AFLP marker was located just over 200 kb from the LjSYM2 gene, the marker SHMT, which was converted from a marker on the pea map, was only 7.9 kb away. The LjSYM2/PsSYM19 region corresponds to two duplicated segments of the Arabidopsis chromosomes AtII and AtIV. Lotus homologues of Arabidopsis genes within these segments were mapped to three clusters on LjI, LjII and LjVI, suggesting that during evolution the genomic segment surrounding LjSYM2 has been subjected to duplication events. However, one marker, AUX-1, was identified based on colinearity between Lotus and Arabidopsis that mapped in physical proximity of the LjSym2 gene.

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Acknowledgements

We thank Thomas Lahaye for useful discussions and Satoko Yoshida, Kate Vickers and Julia Mattner for critical reading of the manuscript. We thank Jillian Perry, Jodie Pike and Julia Schmitz for help with recombinant screens, David Baker, Patrick Bovil and Nigel Hartley for shotgun sequencing of BAC 8M6 and Sara Perkins and Fiona Alderson for plant care. Research at the Sainsbury Laboratory is supported by the Gatsby Charitable Foundation.

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Author notes

  1. M. Koyama

    Present address: John Innes Centre, Department of Crop Genetics, Colney Lane, Norwich NR4 7UH, UK

Authors and Affiliations

  1. The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK

    S. Stracke, M. Koyama & M. Parniske

  2. Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan

    S. Sato, T. Kaneko & S. Tabata

  3. Laboratory of Gene Expression, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark

    N. Sandal

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  1. S. Stracke
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Correspondence to M. Parniske.

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Communicated by J.S. Heslop-Harrison

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Stracke, S., Sato, S., Sandal, N. et al. Exploitation of colinear relationships between the genomes of Lotus japonicus, Pisum sativum and Arabidopsis thaliana, for positional cloning of a legume symbiosis gene. Theor Appl Genet 108, 442–449 (2004). https://doi.org/10.1007/s00122-003-1438-2

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