Cubillos et al. BMC Genomics 2012, 13:117 http://www.biomedcentral.com/1471-2164/13/117 eQTLs were retained after the VBQTL analysis and tabulated based on their gene ontology (GO) classifica- tion. Initially, we selected functional categories with a significant over-representation of eQTLs within the ‘Bio- logical process’ set. For this purpose, we assessed signifi- cance utilising the hypergeometric test (P < 8 × 10-4 after Bonferroni) considering the number of genes within each category at the whole-genome level. Within the selected functional categories, we focused the subse- quent analysis on GO categories containing more than 20 genes. For each category we tested departure from the 1.6:1 ratio (Col:Cvi) using a hypergeometric test. Additional material Additional file 1: eQTL mapping in the Bay × Sha recombinant population [44]. Additional file 2: Table S1. Set of differentially expressed genes between parental accessions Cvi, Bur and Col. Expression differences are reported in log2. Additional file 3: Figure S1. Venn diagram depicting the overlap between genes with differential expression in parental accessions pairs (Cvi vs. Col and Bur vs. Col). Figure S2. Histograms of the explained phenotypic variance (R2; %) for the eQTLs in the a.CviCol and b. BurCol populations. Figure S3. Number of eQTLs per trait. Figure S4. Venn diagram depicting the overlap between probes with local eQTLs in the CviCol and BurCol populations. Figure S5. Histogram of the number of probes with a significant eQTL for different numbers of hidden factors tested with VBQTL in CviCol. Figure S6. Genetic landscape for transcript accumulation variation in BaySha. Figure S7. Histogram of the explained phenotypic variance (R2) for the eQTLs in the BaySha population. Figure S8. Number of eQTLs per trait in BaySha. Figure S9. Distribution of distant-eQTLs along the genome in BaySha. Additional file 4: Table S2. List of eQTLs detected in each cross. Abbreviations: eQTL Chr = chromosome localisation of eQTL, type = eQTL tentative classification (’cis’/’trans’ = local/distant), peak.bp = physical position of the LOD peak, inf.pb = inferior limit, sup.pb = superior limit of supporting physical interval, Add = additive effect (estimated as Xxx-Col, so that a negative allelic effect means Col up- regulated with respect to Xxx), Rsq = variance explained, Rpf = significance. Additional file 5: Table S3. Number of -eQTLs per 1 Mb interval. a. local, b. distant. Additional file 6: Table S4. Overrepresented GO terms within the BurCol distant-hotspots. Additional file 7: Table S5. List of eQTLs detected by VBQTL in CviCol. See Additional file 4: Table S2 for column headings. Acknowledgements This work was supported by ANR grant RILKIT/07-GPLA-07003G and ANR grant ARABIDOSEED/GPLA-007-01. FAC was supported by funding from the European Commission Framework Programme 7, ERC Starting Grant DECODE/ERC-2009-StG-243359 to OL. We thank Michel Caboche and David Bouchez for their support with the ‘Arabidoseed’ grant and discussion of the results and Leopold Parts for the implementation of VBQTL. Author details 1INRA, UMR1318, Institut Jean-Pierre Bourgin, F-78000 Versailles, France. 2Department of Plant Genomics Research, INRA, UMR1165 INRA-CNRS, URGV, F-91057 Evry, France. 3Current address: CEA - DSV - IG - GENOSCOPE, Laboratoire d’Informatique Scientifique, 2 rue Gaston Cremieux, F-91057 Evry, France. 4AgroParisTech, UMR518 INRA Mathematiques et Informatiques Page 11 of 12 Appliquées, Paris, France. 5Current address: Institut de Recherche en Horticulture, Semences INRA/Agrocampus Ouest/Université d’Angers, F- 49071 Beaucouzé, France. Authors’ contributions OL, CC, JPR, LL, SeB and BD designed the study. JY, CC, SeB, BD, SaB and SE handled plant culture for RNA. JY, SE, SaB and MLMM performed the array experiments and initial data analyses. 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