Open Access Highly Accessed Research article

Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail

Laure Frésard12, Sophie Leroux12, Patrice Dehais12, Bertrand Servin12, Hélène Gilbert12, Olivier Bouchez123, Christophe Klopp4, Cédric Cabau5, Florence Vignoles12, Katia Feve12, Amélie Ricros12, David Gourichon6, Christian Diot78, Sabine Richard10119, Christine Leterrier10119, Catherine Beaumont12, Alain Vignal12, Francis Minvielle1314 and Frédérique Pitel12*

Author Affiliations

1 INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan, F-31326, France

2 ENVT, UMR444 Laboratoire de Génétique Cellulaire, Toulouse, F-31076, France

3 INRA, GeT-PlaGe Genotoul, Castanet-Tolosan, F-31326, France

4 INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, F-31326, France

5 INRA, Sigenae, Nouzilly, F-37380, France

6 INRA, PEAT Pôle d'Expérimentation Avicole de Tours, Nouzilly, F- 37380, France

7 INRA, UMR1348 PEGASE, Saint-Gilles, F-35590, France

8 Agrocampus Ouest, UMR1348 PEGASE, Rennes, F-35000, France

9 INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, F-37380, France

10 CNRS, UMR6175 Physiologie de la Reproduction et des Comportements, Nouzilly, F-37380, France

11 Université François Rabelais Tours, UMR Physiologie de la Reproduction et des Comportements, Nouzilly, F-37380, France

12 INRA, UR83 Recherche Avicoles, Nouzilly, F- 37380, France

13 INRA, UMR1313 Génétique animale et biologie intégrative, Jouy en Josas, F-78350, France

14 AgroParisTech, UMR Génétique animale et biologie intégrative, Jouy en Josas, F-78350, France

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BMC Genomics 2012, 13:551  doi:10.1186/1471-2164-13-551

Published: 15 October 2012

Additional files

Additional file 1:

Figure S1. Distribution of the functional annotation of the detected SNP (log scale). Annotations are from the Ensembl APIs (Application Programme Interface): the functional consequence of each SNP in each transcript has been predicted using the Variant Effect Predictor (VEP). All the non intergenic consequences are represented.

Format: PPTX Size: 63KB Download file

Open Data

Additional file 2:

Figure S2. Distribution of the trait in both AIL populations. TI : Tonic Immobility.

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Additional file 3:

Table S1. List of the 384 SNP used in this study.

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Additional file 4:

Table S2. List of the genes localized in the candidate interval. Source : Biomart, Ensembl Genes 61 (Sanger UK), Gallus Gallus Genes (WASHUCS52).

Format: XLSX Size: 13KB Download file

Open Data

Additional file 5:

Figure S3. Quail in a tonic immobility state. Immobilization is induced by keeping the animal on its back in a U-shaped cradle for 10 seconds.

Format: PPTX Size: 223KB Download file

Open Data