Natural allelic variation identifies new genes in the Arabidopsis circadian system

Authors

  • Kamal Swarup,

    1. Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK,
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    • Present address: Plant Science Division, School of Biological Sciences, University Park, Nottingham NG7 2RD, UK.

  • Carlos Alonso-Blanco,

    1. Laboratory of Genetics, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands,
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    • Present address: Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia, Campus Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

  • James R. Lynn,

    1. Horticulture Research International, Wellesbourne CV35 9EF, UK, and
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  • Scott D. Michaels,

    1. Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 5307-1544, USA
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  • Richard M. Amasino,

    1. Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 5307-1544, USA
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  • Maarten Koornneef,

    1. Laboratory of Genetics, Wageningen Agricultural University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands,
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  • Andrew J. Millar

    Corresponding author
    1. Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK,
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*For correspondence (fax +44 24 76523701;
e-mail Andrew.Millar@warwick.ac.uk).

Summary

We have analysed the circadian rhythm of Arabidopsis thaliana leaf movements in the accession Cvi from the Cape Verde Islands, and in the commonly used laboratory strains Columbia (Col) and Landsberg (erecta) (Ler), which originated in Northern Europe. The parental lines have similar rhythmic periods, but the progeny of crosses among them reveal extensive variation for this trait. An analysis of 48 Ler/Cvi recombinant inbred lines (RILs) and a further 30 Ler/Col RILs allowed us to locate four putative quantitative trait loci (QTLs) that control the period of the circadian clock. Near-isogenic lines (NILs) that contain a QTL in a small, defined chromo- somal region allowed us to confirm the phenotypic effect and to map the positions of three period QTLs, designated ESPRESSO, NON TROPPO and RALENTANDO. Quantitative trait loci at the locations of RALENTANDO and of a fourth QTL, ANDANTE, were identified in both Ler/Cvi and Ler/Col RIL populations. Some QTLs for circadian period are closely linked to loci that control flowering time, including FLC. We show that flc mutations shorten the circadian period such that the known allelic variation in the MADS-box gene FLC can account for the ANDANTE QTL. The QTLs ESPRESSO and RALENTANDO identify new genes that regulate the Arabidopsis circadian system in nature, one of which may be the flowering-time gene GIGANTEA.

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