Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

Susanna Atwell, Yu S. Huang, Bjarni J. Vilhjalmsson, Glenda Willems, Matthew Horton, Yan Li, Dazhe Meng, Alexander Platt, Aaron M. Tarone, Tina T. Hu, Rong Jiang, N. Wayan Muliyati, Xu Zhang, Muhammad Ali Amer, Ivan Baxter, Benjamin Brachi, Joanne Chory, Caroline Dean, Marilyne Debieu, Juliette de MeauxJoseph R. Ecker, Nathalie Faure, Joel M. Kniskern, Jonathan D. G. Jones, Todd Michael, Adnane Nemri, Fabrice Roux, David E. Salt, Chunlao Tang, Marco Todesco, M. Brian Traw, Detlef Weigel, Paul Marjoram, Justin O. Borevitz, Joy Bergelson, Magnus Nordborg

Research output: Contribution to journalArticle

1018 Citations (Scopus)

Abstract

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases(1,2), genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits(3). Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.

Original languageEnglish
Pages (from-to)627-631
Number of pages5
JournalNature
Volume465
Issue number7298
DOIs
Publication statusPublished - 3 Jun 2010

Keywords

  • flowering-locus-C
  • linkage disequilibrium
  • population-structure
  • model
  • diseases
  • protein
  • frigida
  • time

Cite this

Atwell, S., Huang, Y. S., Vilhjalmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., Jiang, R., Muliyati, N. W., Zhang, X., Amer, M. A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., ... Nordborg, M. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465(7298), 627-631. https://doi.org/10.1038/nature08800