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Natural variation in light sensitivity of Arabidopsis

Nature Genetics volume 29, pages 441–446 (2001)Cite this article

Abstract

Because plants depend on light for growth, their development and physiology must suit the particular light environment. Plants native to different environments show heritable, apparently adaptive, changes in their response to light1,2. As a first step in unraveling the genetic and molecular basis of these naturally occurring differences, we have characterized intraspecific variation in a light-dependent developmental process—seedling emergence. We examined 141 Arabidopsis thaliana accessions for their response to four light conditions, two hormone conditions and darkness. There was significant variation in all conditions, confirming that Arabidopsis is a rich source of natural genetic diversity. Hierarchical clustering revealed that some accessions had response patterns similar to known photoreceptor mutants, suggesting changes in specific signaling pathways. We found that the unusual far-red response of the Lm-2 accession is due to a single amino-acid change in the phytochrome A (PHYA) protein. This change stabilizes the light-labile PHYA protein in light and causes a 100-fold shift in the threshold for far-red light sensitivity. Purified recombinant Lm-2 PHYA also shows subtle photochemical differences and has a reduced capacity for autophosphorylation. These biochemical changes contrast with previously characterized natural alleles in loci controlling plant development, which result in altered gene expression or loss of gene function3,4,5,6,7,8,9.

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Figure 1: Variation between different strains in response to light and hormones.
Figure 2: Fluence response and hormone dose–response curves.
Figure 3: Hierarchical cluster analysis of light response among accessions.
Figure 4: Characterization of Lm-2.
Figure 5: The Lm-2 change affects PHYB sensitivity to red light.

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Acknowledgements

We thank U. Genick, S. Harmer and J.C. Lagarias for insightful discussion, J.C. Lagarias for Avena PHYA expression constructs, and J. Werner for help with hypocotyl measurements. Seeds were obtained from the Arabidopsis Biological Resource Center (ABRC) at Ohio State University, which is funded by NSF. The joint program in quantitative genetics in the Weigel and Chory laboratories is supported by NIH training grant GM08666 (J.O.B.), by a Helen Hay Whitney Fellowship (J.N.M.), funds from the HHMI and NIH (GM52413) to J.C. and by a grant from Torrey Mesa Research Institute/Syngenta to D.W. D.W. is a Director of the Max Planck Institute. J.C. is an Associate Investigator of the HHMI.

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Author notes

  1. Julin N. Maloof and Justin O. Borevitz: These authors contributed equally to this work.

Authors and Affiliations

  1. Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, 92037, California, USA

    Julin N. Maloof, Justin O. Borevitz, Tsegaye Dabi, Jason Lutes, Ramlah B. Nehring, Joanna L. Redfern, Gabriel T. Trainer, Jeanne M. Wilson, Detlef Weigel & Joanne Chory

  2. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, 92037, California, USA

    Jason Lutes, Gabriel T. Trainer & Joanne Chory

  3. Institute of Physical and Chemical Research (RIKEN), Wako-shi, 351-0198, Saitama, Japan

    Tadao Asami

  4. Department of Family/Preventive Medicine, University of California San Diego, La Jolla, 92093, California, USA

    Charles C. Berry

  5. Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany

    Detlef Weigel

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  1. Julin N. Maloof
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Correspondence to Detlef Weigel.

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Maloof, J., Borevitz, J., Dabi, T. et al. Natural variation in light sensitivity of Arabidopsis. Nat Genet 29, 441–446 (2001). https://doi.org/10.1038/ng777

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