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

Additional files

Additional file 1:

eQTL mapping in the Bay × Sha recombinant population [44].

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Additional file 2:

Table S1. Set of differentially expressed genes between parental accessions Cvi, Bur and Col. Expression differences are reported in log2.

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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.

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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.

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Additional file 5:

Table S3. Number of -eQTLs per 1 Mb interval. a. local, b. distant.

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Additional file 6:

Table S4. Overrepresented GO terms within the BurCol distant-hotspots.

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Additional file 7:

Table S5. List of eQTLs detected by VBQTL in CviCol. See Additional file 4: Table S2 for column headings.

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