Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes

Autor: Claudia Bartoli, Carine Huard-Chauveau, Hana Lee, Fabrice Roux, Miaoyan Wang, Dominique Roby, Mary Sara McPeek, Christopher Meyer, Joy Bergelson
Přispěvatelé: Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Invertebrate Zoology, Smithsonian Institution-National Museum of Natural History, Department of Ecology and Evolution [Chicago], University of Chicago, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Franco-American Fulbright Commission (Program Nord Pas de Calais), Region Midi-Pyrenees (project Accueil de nouvelles equipes d'excellence), Agence Nationale de la Recherche (ANR) projects RIPOSTE : ANR-14-CE19-0024-01, Laboratoire d'Excellence (LABEX) Towards a Unified Theory of Biotic Interactions: Role of Environmental Pertubations (TULIP) : ANR-10-LABX-41, ANR-11-IDEX-0002-02, National Institutes of Health : R01 HG001645, R01 GM083068, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2018, ⟨10.1073/pnas.1710980115⟩
Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2018, 115 (24), pp.E5440-E5449. ⟨10.1073/pnas.1710980115⟩
Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (24), pp.E5440-E5449. ⟨10.1073/pnas.1710980115⟩
ISSN: 0027-8424
1091-6490
DOI: 10.1073/pnas.1710980115⟩
Popis: Infectious diseases are often affected by specific pairings of hosts and pathogens and therefore by both of their genomes. The integration of a pair of genomes into genome-wide association mapping can provide an exquisitely detailed view of the genetic landscape of complex traits. We present a statistical method, ATOMM (Analysis with a Two-Organism Mixed Model), that maps a trait of interest to a pair of genomes simultaneously; this method makes use of whole-genome sequence data for both host and pathogen organisms. ATOMM uses a two-way mixed-effect model to test for genetic associations and cross-species genetic interactions while accounting for sample structure including interactions between the genetic backgrounds of the two organisms. We demonstrate the applicability of ATOMM to a joint association study of quantitative disease resistance (QDR) in the Arabidopsis thaliana-Xanthomonas arboricola pathosystem. Our method uncovers a clear host-strain specificity in QDR and provides a powerful approach to identify genetic variants on both genomes that contribute to phenotypic variation.
Databáze: OpenAIRE
Externí odkaz: