title: Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken.
abstract: In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.
authors.affiliation: INRA, UMR1348 PEGASE, Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, France; Université Européenne de Bretagne, Rennes, France.
authors.forename: Pierre-François
authors.initials: PF
authors.lastname: Roux
authors.affiliation: INRA, UMR1348 PEGASE, Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, France; Université Européenne de Bretagne, Rennes, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Boutin
authors.affiliation: INRA, UMR1348 PEGASE, Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, France; Université Européenne de Bretagne, Rennes, France.
authors.forename: Colette
authors.initials: C
authors.lastname: Désert
authors.affiliation: INRA, SIGENAE, Castanet-Tolosan, France.
authors.forename: Anis
authors.initials: A
authors.lastname: Djari
authors.affiliation: INRA, UMR1388 GenPhySE, GeT-PlaGe, Castanet-Tolosan, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: INRA, SIGENAE, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: INRA, UMR1348 PEGASE, Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, France; Université Européenne de Bretagne, Rennes, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
authors.affiliation: INRA, UMR1348 PEGASE, Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Demeure
mesh_terms: D050154:Adiposity / Q000235:genetics*; D000818:Animals; D002645:Chickens; D002874:Chromosome Mapping; D056726:Genetic Association Studies; D008040:Genetic Linkage; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D009765:Obesity / Q000235:genetics* / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*