Open Access Research article

Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures

Francisco A Cubillos1, Jennifer Yansouni12, Hamid Khalili13, Sandrine Balzergue2, Samira Elftieh2, Marie-Laure Martin-Magniette24, Yann Serrand1, Loïc Lepiniec1, Sébastien Baud1, Bertrand Dubreucq1, Jean-Pierre Renou25, Christine Camilleri1* and Olivier Loudet1*

Author Affiliations

1 INRA, UMR1318, Institut Jean-Pierre Bourgin, F-78000 Versailles, France

2 Department of Plant Genomics Research, INRA, UMR1165 INRA-CNRS, URGV, F-91057 Evry, France

3 Current address: CEA - DSV - IG - GENOSCOPE, Laboratoire d'Informatique Scientifique, 2 rue Gaston Cremieux, F-91057 Evry, France

4 AgroParisTech, UMR518 INRA Mathematiques et Informatiques Appliquées, Paris, France

5 Current address: Institut de Recherche en Horticulture, Semences INRA/Agrocampus Ouest/Université d'Angers, F-49071 Beaucouzé, France

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BMC Genomics 2012, 13:117  doi:10.1186/1471-2164-13-117

Published: 27 March 2012



Expression traits can vary quantitatively between individuals and have a complex inheritance. Identification of the genetics underlying transcript variation can help in the understanding of phenotypic variation due to genetic factors regulating transcript abundance and shed light into divergence patterns. So far, only a limited number of studies have addressed this subject in Arabidopsis, with contrasting results due to dissimilar statistical power. Here, we present the transcriptome architecture in leaf tissue of two RIL sets obtained from a connected-cross design involving 3 commonly used accessions. We also present the transcriptome architecture observed in developing seeds of a third independent cross.


The utilisation of the novel R/eqtl package (which goal is to automatize and extend functions from the R/qtl package) allowed us to map 4,290 and 6,534 eQTLs in the Cvi-0 × Col-0 and Bur-0 × Col-0 recombinant populations respectively. In agreement with previous studies, we observed a larger phenotypic variance explained by eQTLs in linkage with the controlled gene (potentially cis-acting), compared to distant loci (acting necessarily indirectly or in trans). Distant eQTLs hotspots were essentially not conserved between crosses, but instead, cross-specific. Accounting for confounding factors using a probabilistic approach (VBQTL) increased the mapping resolution and the number of significant associations. Moreover, using local eQTLs obtained from this approach, we detected evidence for a directional allelic effect in genes with related function, where significantly more eQTLs than expected by chance were up-regulated from one of the accessions. Primary experimental data, analysis parameters, eQTL results and visualisation of LOD score curves presented here are stored and accessible through the QTLstore service database webcite.


Our results demonstrate the extensive diversity and moderately conserved eQTL landscape between crosses and validate the utilisation of expression traits to explore for candidates behind phenotypic variation among accessions. Furthermore, this stresses the need for a wider spectrum of diversity to fully understand expression trait variation within a species.

eQTL; Natural variation; Selection; RILs