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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

Abstract

Background

As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.

Results

The sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.

Conclusions

These data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix.

Keywords:
Quail; Tonic immobility; Sequencing; AFLP; Transcripts; SNP; AIL