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Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis

Nature Genetics volume 46, pages 77–81 (2014)Cite this article

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Abstract

With the increased availability of high-resolution sequence information, genome-wide association (GWA) studies have become feasible in a number of species1,2,3,4,5,6,7,8. The vast majority of these studies are conducted in human populations, where it is difficult to provide strong evidence for the functional involvement of unknown genes that are identified using GWA. Here we used the model organism Arabidopsis thaliana to combine high-throughput confocal microscopy imaging of traits at the cellular level, GWA and expression analyses to identify genomic regions that are associated with developmental cell–type traits. We identify and characterize a new F-box gene, KUK, that regulates meristem and cell length. We further show that polymorphisms in the coding sequence are the major causes of KUK allele–dependent natural variation in root development. This work demonstrates the feasibility of GWA using cellular traits to identify causal genes for basic biological processes such as development.

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Figure 1: Root traits at the cellular level.
Figure 2: GWA data.
Figure 3: The role of KUK.
Figure 4: Allele dependency of KUK function and protein localization.

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Change history

  • 26 November 2013

    In the version of this article initially published online, there was an error in the final paragraph of the main text. Specifically, the phrase "previously known regulators" should have appeared as "previously unknown regulators." The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We are grateful for assistance in the GWA analysis and access to software from A. Korte, Ü. Seren, B. Vilhjalmsson and M. Nordborg and for technical assistance from B. Wohlrab and C. Göschl. We thank P. Benfey, T. Greb, M. Nordborg, L. Valledor, A. Korte, D. Filiault and members of the Busch laboratory for valuable discussions and critical reading of the manuscript. We thank V. Nizhynska, P. Korte and M. Nordborg (Gregor Mendel Institute, Vienna, Austria) for donating seeds for natural accession, S. Waidmann, P. Sánchez and J. Agustí (Gregor Mendel Institute, Vienna, Austria) for materials and advice on vectors and cloning and T. Friese for manuscript editing. This research was supported by funds from the Austrian Academy of Science through the Gregor Mendel Institute and a European Molecular Biology Organization (EMBO) long-term fellowship to T.T.

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  1. Mónica Meijón

    Present address: Present address: Regional Institute for Research and Agro-Food Development (SERIDA), Forest Research Program, 'La Mata' Experimental Station, Grado-Asturias, Spain.,

Authors and Affiliations

  1. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria

    Mónica Meijón, Santosh B Satbhai, Takashi Tsuchimatsu & Wolfgang Busch

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  1. Mónica Meijón
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Contributions

T.T. carried out the population genetic analyses. S.B.S. performed the experiments with the transgenic KUK lines. M.M. performed the phenotyping, trait quantification, qRT-PCRs and cloning. W.B. conducted KUK-YFP reporter line analyses. W.B. and M.M. conceived the experiments, analyzed the data and wrote the paper.

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Correspondence to Wolfgang Busch.

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The authors declare no competing financial interests.

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Meijón, M., Satbhai, S., Tsuchimatsu, T. et al. Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis. Nat Genet 46, 77–81 (2014). https://doi.org/10.1038/ng.2824

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