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 Meaux & 16 others Joseph 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

959 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., ... 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

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. / Atwell, Susanna; Huang, Yu S.; Vilhjalmsson, Bjarni J.; Willems, Glenda; Horton, Matthew; Li, Yan; Meng, Dazhe; Platt, Alexander; Tarone, Aaron M.; Hu, Tina T.; Jiang, Rong; Muliyati, N. Wayan; Zhang, Xu; Amer, Muhammad Ali; Baxter, Ivan; Brachi, Benjamin; Chory, Joanne; Dean, Caroline; Debieu, Marilyne; de Meaux, Juliette; Ecker, Joseph R.; Faure, Nathalie; Kniskern, Joel M.; Jones, Jonathan D. G.; Michael, Todd; Nemri, Adnane; Roux, Fabrice; Salt, David E.; Tang, Chunlao; Todesco, Marco; Traw, M. Brian; Weigel, Detlef; Marjoram, Paul; Borevitz, Justin O.; Bergelson, Joy; Nordborg, Magnus.

In: Nature, Vol. 465, No. 7298, 03.06.2010, p. 627-631.

Research output: Contribution to journalArticle

Atwell, S, Huang, YS, Vilhjalmsson, BJ, Willems, G, Horton, M, Li, Y, Meng, D, Platt, A, Tarone, AM, Hu, TT, Jiang, R, Muliyati, NW, Zhang, X, Amer, MA, Baxter, I, Brachi, B, Chory, J, Dean, C, Debieu, M, de Meaux, J, Ecker, JR, Faure, N, Kniskern, JM, Jones, JDG, Michael, T, Nemri, A, Roux, F, Salt, DE, Tang, C, Todesco, M, Traw, MB, Weigel, D, Marjoram, P, Borevitz, JO, Bergelson, J & Nordborg, M 2010, 'Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines', Nature, vol. 465, no. 7298, pp. 627-631. https://doi.org/10.1038/nature08800
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Jun 3;465(7298):627-631. https://doi.org/10.1038/nature08800
Atwell, Susanna ; Huang, Yu S. ; Vilhjalmsson, Bjarni J. ; Willems, Glenda ; Horton, Matthew ; Li, Yan ; Meng, Dazhe ; Platt, Alexander ; Tarone, Aaron M. ; Hu, Tina T. ; Jiang, Rong ; Muliyati, N. Wayan ; Zhang, Xu ; Amer, Muhammad Ali ; Baxter, Ivan ; Brachi, Benjamin ; Chory, Joanne ; Dean, Caroline ; Debieu, Marilyne ; de Meaux, Juliette ; Ecker, Joseph R. ; Faure, Nathalie ; Kniskern, Joel M. ; Jones, Jonathan D. G. ; Michael, Todd ; Nemri, Adnane ; Roux, Fabrice ; Salt, David E. ; Tang, Chunlao ; Todesco, Marco ; Traw, M. Brian ; Weigel, Detlef ; Marjoram, Paul ; Borevitz, Justin O. ; Bergelson, Joy ; Nordborg, Magnus. / Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. In: Nature. 2010 ; Vol. 465, No. 7298. pp. 627-631.
@article{253dec640ac3413e8b01020a72744998,
title = "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines",
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.",
keywords = "flowering-locus-C, linkage disequilibrium, population-structure, model, diseases, protein, frigida, time",
author = "Susanna Atwell and Huang, {Yu S.} and Vilhjalmsson, {Bjarni J.} and Glenda Willems and Matthew Horton and Yan Li and Dazhe Meng and Alexander Platt and Tarone, {Aaron M.} and Hu, {Tina T.} and Rong Jiang and Muliyati, {N. Wayan} and Xu Zhang and Amer, {Muhammad Ali} and Ivan Baxter and Benjamin Brachi and Joanne Chory and Caroline Dean and Marilyne Debieu and {de Meaux}, Juliette and Ecker, {Joseph R.} and Nathalie Faure and Kniskern, {Joel M.} and Jones, {Jonathan D. G.} and Todd Michael and Adnane Nemri and Fabrice Roux and Salt, {David E.} and Chunlao Tang and Marco Todesco and Traw, {M. Brian} and Detlef Weigel and Paul Marjoram and Borevitz, {Justin O.} and Joy Bergelson and Magnus Nordborg",
year = "2010",
month = "6",
day = "3",
doi = "10.1038/nature08800",
language = "English",
volume = "465",
pages = "627--631",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7298",

}

TY - JOUR

T1 - Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

AU - Atwell, Susanna

AU - Huang, Yu S.

AU - Vilhjalmsson, Bjarni J.

AU - Willems, Glenda

AU - Horton, Matthew

AU - Li, Yan

AU - Meng, Dazhe

AU - Platt, Alexander

AU - Tarone, Aaron M.

AU - Hu, Tina T.

AU - Jiang, Rong

AU - Muliyati, N. Wayan

AU - Zhang, Xu

AU - Amer, Muhammad Ali

AU - Baxter, Ivan

AU - Brachi, Benjamin

AU - Chory, Joanne

AU - Dean, Caroline

AU - Debieu, Marilyne

AU - de Meaux, Juliette

AU - Ecker, Joseph R.

AU - Faure, Nathalie

AU - Kniskern, Joel M.

AU - Jones, Jonathan D. G.

AU - Michael, Todd

AU - Nemri, Adnane

AU - Roux, Fabrice

AU - Salt, David E.

AU - Tang, Chunlao

AU - Todesco, Marco

AU - Traw, M. Brian

AU - Weigel, Detlef

AU - Marjoram, Paul

AU - Borevitz, Justin O.

AU - Bergelson, Joy

AU - Nordborg, Magnus

PY - 2010/6/3

Y1 - 2010/6/3

N2 - 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.

AB - 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.

KW - flowering-locus-C

KW - linkage disequilibrium

KW - population-structure

KW - model

KW - diseases

KW - protein

KW - frigida

KW - time

U2 - 10.1038/nature08800

DO - 10.1038/nature08800

M3 - Article

VL - 465

SP - 627

EP - 631

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7298

ER -