Academic Journal
Recovering power in Association Mapping Panels with variable levels of linkage disequilibrium
| العنوان: | Recovering power in Association Mapping Panels with variable levels of linkage disequilibrium |
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| المؤلفون: | Rincent, Renaud, Moreau, Laurence, Monod, Hervé, Kuhn, Estelle, Melchinger, Albrecht E, Malvar, Rosa A, Moreno-Gonzalez, Jesus, Nicolas, Stephane, S., Madur, Delphine, D., Combes, Valerie, V., Dumas, Fabrice, F., Altmann, Thomas, Brunel, Dominique, D., Ouzunova, Milena, Flament, Pascal, Dubreuil, Pierre, Charcosset, Alain, A., Mary-Huard, Tristan |
| المساهمون: | Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Genetics and Genomics in Cereals, BIOGEMMA, KWS SAAT SE & Co.KGaA, Groupe Limagrain, Unité de biométrie et intelligence artificielle de Jouy (MIA-JOUY), Institut National de la Recherche Agronomique (INRA), Institute of Plant Breeding, Seed Science and Population Genetics, Universität Hohenheim = University of Hohenheim, Mision Biologica de Galicia (MBG), Consejo Superior de Investigaciones Cientificas España = Spanish National Research Council Spain (CSIC), Instituto Galego da Calidade Alimentaria (INGACAL), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Etude du Polymorphisme des Génomes Végétaux (EPGV), French National Agency for Research (ANR), German Federal Ministry of Education and Research (BMBF), Spanish ministry of Science and Innovation (MICINN) EUI2008-3635, Limagrain, Biogemma, Kleinwanzlebener Saatzucht, French ANRt, ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010) |
| المصدر: | ISSN: 0016-6731 ; Genetics ; https://hal.inrae.fr/hal-02634244 ; Genetics, 2014, 197 (1), pp.375-387. ⟨10.1534/genetics.113.159731⟩. |
| بيانات النشر: | CCSD Oxford University Press |
| سنة النشر: | 2014 |
| المجموعة: | Institut National de la Recherche Agronomique: ProdINRA |
| مصطلحات موضوعية: | Association mapping, Zea mays L, kinship, linkage disequilibrium, power, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology |
| الوصف: | International audience ; Association mapping has permitted the discovery of major QTLs in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We studied analytically power in association studies by computing non-centrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high Linkage Disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimate the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers located on other chromosomes than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and more powerful than classical models. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/24532779; PRODINRA: 258042; PUBMED: 24532779; PUBMEDCENTRAL: PMC4012494; WOS: 000335858900028 |
| DOI: | 10.1534/genetics.113.159731 |
| الاتاحة: | https://hal.inrae.fr/hal-02634244 https://doi.org/10.1534/genetics.113.159731 |
| رقم الانضمام: | edsbas.BB4772C6 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1534/genetics.113.159731 |
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