Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines (original) (raw)

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Acknowledgements

We thank B. Carvalho for his advice on how to modify the OLIGO package. This work was primarily supported by US National Science Foundation (NSF) grant DEB-0519961 (J.B., M.N.), US National Institutes of Health (NIH) grant GM073822 (J.O.B.), and NSF grant DEB-0723935 (M.N.). Additional support was provided by the Dropkin Foundation, NIH grant GM057994 and NSF grant MCB-0603515 (J.B.), the Max Planck Society (D.W., M.T.), the Austrian Academy of Sciences (M.N.), the University of Lille 1 (F.R.), NIH grant GM078536 and NIH grant P42ES007373 (D.E.S.), NIH grant GM62932 (J.C., D.W.), the Howard Hughes Medical Institute (J.C.), the Deutsche Forschungsgemeinschaft (DFG) SFB 680 (J.d.M.), a Marie Curie International Outgoing Fellowship ‘ANAVACO’ (project number 220833; G.W.), and a Gottfried Wilhelm Leibniz Award of the DFG (D.W.). The project would not have been possible without the existence of The Arabidopsis Information Resource (http://arabidopsis.org).

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Author notes

1. Susanna Atwell, Yu S. Huang, Bjarni J. Vilhjálmsson and Glenda Willems: These authors contributed equally to this work.

Authors and Affiliations

1. Molecular and Computational Biology,,
   Susanna Atwell, Yu S. Huang, Bjarni J. Vilhjálmsson, Glenda Willems, Dazhe Meng, Alexander Platt, Aaron M. Tarone, Tina T. Hu, Rong Jiang, Muhammad Ali Amer, Chunlao Tang & Magnus Nordborg
2. Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA,
   Paul Marjoram
3. Department of Ecology & Evolution, University of Chicago, Chicago, Illinois 60637, USA,
   Matthew Horton, Yan Li, N. Wayan Muliyati, Xu Zhang, Joel M. Kniskern, Fabrice Roux, M. Brian Traw, Justin O. Borevitz & Joy Bergelson
4. Bindley Bioscience Center,,
   Ivan Baxter
5. Purdue University, West Lafayette, Indiana 47907, USA ,
   David E. Salt
6. Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille 1, F-59655 Villeneuve d’Ascq Cedex, France
   Benjamin Brachi, Nathalie Faure & Fabrice Roux
7. Howard Hughes Medical Institute, La Jolla, California 92037, USA ,
   Joanne Chory
8. Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA ,
   Joanne Chory, Joseph R. Ecker & Todd Michael
9. Department of Cell and Development Biology, John Innes Centre, Norwich NR4 7UH, UK
   Caroline Dean
10. Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
    Marilyne Debieu & Juliette de Meaux
11. Sainsbury Laboratory, Norwich NR4 7UH, UK
    Jonathan D. G. Jones & Adnane Nemri
12. Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
    Marco Todesco & Detlef Weigel
13. Gregor Mendel Institute, A-1030 Vienna, Austria
    Magnus Nordborg

Authors

1. Susanna Atwell
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2. Yu S. Huang
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3. Bjarni J. Vilhjálmsson
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4. Glenda Willems
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5. Matthew Horton
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6. Yan Li
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7. Dazhe Meng
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8. Alexander Platt
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9. Aaron M. Tarone
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10. Tina T. Hu
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11. Rong Jiang
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12. N. Wayan Muliyati
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13. Xu Zhang
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14. Muhammad Ali Amer
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15. Ivan Baxter
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16. Benjamin Brachi
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17. Joanne Chory
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18. Caroline Dean
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19. Marilyne Debieu
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20. Juliette de Meaux
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21. Joseph R. Ecker
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22. Nathalie Faure
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23. Joel M. Kniskern
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24. Jonathan D. G. Jones
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25. Todd Michael
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26. Adnane Nemri
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27. Fabrice Roux
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28. David E. Salt
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29. Chunlao Tang
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30. Marco Todesco
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31. M. Brian Traw
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32. Detlef Weigel
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33. Paul Marjoram
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34. Justin O. Borevitz
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35. Joy Bergelson
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36. Magnus Nordborg
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Contributions

J.O.B., J.B. and M.N. are equal senior authors. J.R.E. and D.W. generated the SNPs used in this project. S.A., M.H., Y.L., N.W.M., X.Z., J.O.B. and J.B. were responsible for the experimental aspects of genotyping. Y.S.H., B.J.V., M.H., T.T.H., R.J., X.Z., M.A.A., P.M., J.O.B., J.B. and M.N. were responsible for data management and the bioinformatics pipeline. S.A., I.B., B.B., J.C., C.D., M.D., J.d.M., N.F., J.M.K., J.D.G.J., T.M., A.N., F.R., D.E.S., C.T., M.T., M.B.T., D.W., J.B. and M.N. were responsible for phenotyping. S.A., Y.S.H., B.J.V., G.W., D.M., A.P., A.M.T., P.M. and M.N carried out the GWA analyses. Y.S.H. and D.M. developed the project website. M.N. wrote the paper with significant contributions from S.A., Y.S.H., B.J.V., G.W., A.P. and J.B. J.O.B., J.B. and M.N. designed and supervised the project.

Corresponding author

Correspondence toMagnus Nordborg.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Information which comprises: 1 Genotyping; 2 Association Mapping Methods; 3 Enrichment for a priori candidates, Supplementary Figures 1-152 with legends, Supplementary References and Supplementary Tables 1-7. (PDF 35247 kb)

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Atwell, S., Huang, Y., Vilhjálmsson, B. et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.Nature 465, 627–631 (2010). https://doi.org/10.1038/nature08800

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• Received: 23 June 2009
• Accepted: 30 December 2009
• Published: 24 March 2010
• Issue Date: 03 June 2010
• DOI: https://doi.org/10.1038/nature08800