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

Author

Listed:
  • Susanna Atwell

    (Molecular and Computational Biology,)

  • Yu S. Huang

    (Molecular and Computational Biology,)

  • Bjarni J. Vilhjálmsson

    (Molecular and Computational Biology,)

  • Glenda Willems

    (Molecular and Computational Biology,)

  • Matthew Horton

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Yan Li

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Dazhe Meng

    (Molecular and Computational Biology,)

  • Alexander Platt

    (Molecular and Computational Biology,)

  • Aaron M. Tarone

    (Molecular and Computational Biology,)

  • Tina T. Hu

    (Molecular and Computational Biology,)

  • Rong Jiang

    (Molecular and Computational Biology,)

  • N. Wayan Muliyati

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Xu Zhang

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Muhammad Ali Amer

    (Molecular and Computational Biology,)

  • Ivan Baxter

    (Bindley Bioscience Center,)

  • Benjamin Brachi

    (Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille 1)

  • Joanne Chory

    (Howard Hughes Medical Institute, La Jolla, California 92037, USA
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA)

  • Caroline Dean

    (John Innes Centre)

  • Marilyne Debieu

    (Max Planck Institute for Plant Breeding Research)

  • Juliette de Meaux

    (Max Planck Institute for Plant Breeding Research)

  • Joseph R. Ecker

    (Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA)

  • Nathalie Faure

    (Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille 1)

  • Joel M. Kniskern

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Jonathan D. G. Jones

    (Sainsbury Laboratory)

  • Todd Michael

    (Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA)

  • Adnane Nemri

    (Sainsbury Laboratory)

  • Fabrice Roux

    (University of Chicago, Chicago, Illinois 60637, USA
    Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille 1)

  • David E. Salt

    (Purdue University, West Lafayette, Indiana 47907, USA)

  • Chunlao Tang

    (Molecular and Computational Biology,)

  • Marco Todesco

    (Max Planck Institute for Developmental Biology)

  • M. Brian Traw

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Detlef Weigel

    (Max Planck Institute for Developmental Biology)

  • Paul Marjoram

    (Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA)

  • Justin O. Borevitz

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Joy Bergelson

    (University of Chicago, Chicago, Illinois 60637, USA)

  • Magnus Nordborg

    (Molecular and Computational Biology,
    Gregor Mendel Institute)

Abstract

The genetics of plant variety Large-scale genome-wide association (GWA) studies have become an important tool in human genomics, mostly focused on disease but also on adaptive variations such as skin colour. The technique is now shown to be similarly useful in plants. Atwell et al. report a GWA study of over a hundred phenotypes in naturally occurring inbred lines of Arabidopsis thaliana. The results range from significant associations, usually for single genes, to more difficult-to-interpret findings that indicate confounding by complex genetics and population structure. The accompanying paper by Todesco et al. demonstrates the ability of this technique to detect major-effect gene loci. Using forward genetics and GWA analyses, they show that variation at a single locus (ACD6) in Arabidopsis underlies phenotypic variation in vegetative growth as well as resistance to infection. The strong enhancement of resistance mediated by one of the alleles at this locus explains its persistence in natural populations throughout the world, despite it drastically reducing new leaf production.

Suggested Citation

  • Susanna Atwell & Yu S. Huang & Bjarni J. Vilhjálmsson & Glenda Willems & Matthew Horton & Yan Li & Dazhe Meng & Alexander Platt & Aaron M. Tarone & Tina T. Hu & Rong Jiang & N. Wayan Muliyati & Xu Zha, 2010. "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines," Nature, Nature, vol. 465(7298), pages 627-631, June.
    • Handle: RePEc:nat:nature:v:465:y:2010:i:7298:d:10.1038_nature08800
    DOI: 10.1038/nature08800
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    Cited by:

    1. Muhammad Saeed & Farhan Ullah & Liaqat Shah & Waqas Ahmad & Murad Ali & Fazal Munsif & Ahmad Zubair & Muhammad Ibrahim & Syed Mushtaq Ahmed Shah & Hammad Uddin & Chen Can & Si Hongqi & Ma Chuanxi, 2022. "Identification of Three Novel QTLs Associated with Yellow Rust Resistance in Wheat ( Triticum aestivum L.) Anong-179/Khaista-17 F 2 Population," Sustainability, MDPI, vol. 14(12), pages 1-15, June.
    2. Minghui Kang & Haolin Wu & Huanhuan Liu & Wenyu Liu & Mingjia Zhu & Yu Han & Wei Liu & Chunlin Chen & Yan Song & Luna Tan & Kangqun Yin & Yusen Zhao & Zhen Yan & Shangling Lou & Yanjun Zan & Jianquan , 2023. "The pan-genome and local adaptation of Arabidopsis thaliana," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Huang, Lucy & Buzbas, Erkan O. & Rosenberg, Noah A., 2013. "Genotype imputation in a coalescent model with infinitely-many-sites mutation," Theoretical Population Biology, Elsevier, vol. 87(C), pages 62-74.
    4. Yuxuan Duan & Hongliang Zheng & Haoran Wen & Di Qu & Jingnan Cui & Chong Li & Jingguo Wang & Hualong Liu & Luomiao Yang & Yan Jia & Wei Xin & Shuangshuang Li & Detang Zou, 2022. "Identification of Candidate Genes for Salt Tolerance at the Germination Stage in Japonica Rice by Genome-Wide Association Analysis," Agriculture, MDPI, vol. 12(10), pages 1-15, October.
    5. Ganwen Zhang & Jianini Zhao & Jieru Wang & Guo Lin & Lin Li & Fengfei Ban & Meiting Zhu & Yangjun Wen & Jin Zhang, 2024. "An Improved Expectation–Maximization Bayesian Algorithm for GWAS," Mathematics, MDPI, vol. 12(13), pages 1-14, June.
    6. Hideki Yoshida & Ko Hirano & Kenji Yano & Fanmiao Wang & Masaki Mori & Mayuko Kawamura & Eriko Koketsu & Masako Hattori & Reynante Lacsamana Ordonio & Peng Huang & Eiji Yamamoto & Makoto Matsuoka, 2022. "Genome-wide association study identifies a gene responsible for temperature-dependent rice germination," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Hanne De Kort & Sylvain Legrand & Olivier Honnay & James Buckley, 2022. "Transposable elements maintain genome-wide heterozygosity in inbred populations," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Yasuhiro Sato & Rie Shimizu-Inatsugi & Kazuya Takeda & Bernhard Schmid & Atsushi J. Nagano & Kentaro K. Shimizu, 2024. "Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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