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Cited by 1,780Genetic Mapping and Diversity in Plants and AnimalsGenetic Associations and EpidemiologyGenetic and phenotypic traits in livestock

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

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Atwell, Susanna, Huang, Yu S., Vilhjálmsson, Bjarni J., Willems, Glenda, Horton, Matthew, Li, Yan, Meng, Dazhe, Platt, Alexander +28 more·2010·Nature
DOI 10.1038/nature08800PMC PMC3023908
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Abstract

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, 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. 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.

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  • Glucosinolates may also regulate circadian clock and flowering time.

    “Apart from growth and stomatal opening, glucosinolates may also regulate the circadian clock and flowering time.”

    From Plant Secondary Metabolites as Defenses, Regulators, and Primary Metabolites: The Blurred Functional Trichotomy (2020) · cites this paper as Atwell et al., 2010

    The paper’s flowering-related results (Abstract section; page unavailable) discuss associations involving FRI, FLC, and DOG1, but do not link glucosinolates to flowering time. Searches for glucosinolates, the circadian clock, and flowering together found no passage addressing the claimed regulatory role. (LLM, conf=0.72)

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Cites

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Research works printed but not linked: 25

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Authors
Atwell, S., Huang, Y. S., Vilhjálmsson, 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., de Meaux, J., Ecker, J. R., Faure, N., Kniskern, J. M., Jones, J. D. G., Michael, T., Nemri, A., Roux, F., Salt, D. E., Tang, C., Todesco, M., Traw, M. B., Weigel, D., Marjoram, P., Borevitz, J. O., Bergelson, J., & Nordborg, M.
Affiliations
  • University of Southern California (US)
  • University of Chicago (US)
  • Centre National de la Recherche Scientifique (FR)
  • Salk Institute for Biological Studies (US)
  • John Innes Centre (GB)
  • Max Planck Institute for Plant Breeding Research (DE)
  • Sainsbury Laboratory (GB)
  • Purdue University West Lafayette (US)
  • Max Planck Institute for Developmental Biology (DE)
  • Gregor Mendel Institute of Molecular Plant Biology (AT)
Corresponding author
Nordborg, Magnus
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2010-03-24
Volume
465
Issue
7298
Pages
627-631
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature08800
PMC
PMC3023908
OpenAlex
W2137797806
Cited by
1,780
References
4
Citations by year
2026: 48 · 2025: 58 · 2024: 90 · 2023: 77 · 2022: 123 · 2021: 111 · 2020: 112 · 2019: 105 · 2018: 115 · 2017: 126 · 2016: 146 · 2015: 137 · 2014: 124 · 2013: 136 · 2012: 124
FWCI
73.10
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • HAL (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • Max Planck Digital Library (submittedVersion)
  • ANU Open Research (Australian National University) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • Biotechnology and Biological Sciences Research Council (BBS/E/J/000CA355)
  • National Institute of General Medical Sciences (GM073822, R01GM057994, GM057994, GM 62932, R01GM073822, GM078536, R01GM078536, R01GM062932)
  • National Institute of Environmental Health Sciences (P42ES007373)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords
genome-wide association study, Arabidopsis thaliana, inbred lines, natural genetic variation, phenotypic variability, population structure, major-effect loci, disease resistance, vegetative growth, forward genetics, candidate genes, plant genetics, false positive association
MeSH terms
Alleles, Genotype, Immunity, Innate, Inbreeding, Phenotype, Genes, Plant, Arabidopsis, Genome, Plant, Polymorphism, Single Nucleotide, Arabidopsis Proteins, Flowers, Genome-Wide Association Study, Genetic Loci

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