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Genetics, Vol. 178, 2253-2264, April 2008, Copyright © 2008
doi:10.1534/genetics.107.083899

Quantitative Trait Loci Mapping in Five New Large Recombinant Inbred Line Populations of Arabidopsis thaliana Genotyped With Consensus Single-Nucleotide Polymorphism Markers

Matthieu Simon*, Olivier Loudet*, Stéphanie Durand*, Aurélie Bérard{dagger}, Dominique Brunel{dagger}, François-Xavier Sennesal*, Mylène Durand-Tardif*, Georges Pelletier* and Christine Camilleri*,1

* Station de Génétique et d'Amélioration des Plantes UR254, INRA, F-78000 Versailles, France and {dagger} Etude du Polymorphisme des Génomes Végétaux UR1279, INRA, F-91000 Evry, France

1 Corresponding author: Station de Génétique et d'Amélioration des Plantes UR254, INRA, Rte. de St. Cyr, F-78000 Versailles, France.
E-mail: camiller{at}versailles.inra.fr

Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions >7%.




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