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Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay

INRA GABI Unit

GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

The project « A thousand Gallus genomes» : sharing sequene data for their improved use.

@ CC. Productions Animales M. Tixier-Boichard, F. Hérault, P. Bardou, C. Klopp
Whole genome sequencing has changed many fields in genetics: selection, biodiversity, understanding the genotype-phenotype relationship. The idea of a "1000 Genomes" project, tested in cattle, consists of sharing sequence data obtained by different partners to facilitate the extraction of information that answers the different research questions. Here we present how this will be done for the chicken on both national and international levels.

Whole genome sequencing has become much more attainable in the chicken. The "Thousand Gallus Genomes" projct is aimed at gathering Gallus genera sequences that have been produced by research projects. The importance is to increase the strength of the genomic analyses by increasing the number of genomes compared. Possible applications concern the genome structure, the overall characterization of the species diversity, identification of causal mutations and help for genomic selection.

This review first describes the context of chicken genomics before developping the "Thousand Genomes" concept, illustrates it with a project coordinated by French teams and presents how it can be extended.

The French project includes 207 individual sequences for 8 research projects with public financing, on a large scale of populations (broiler chickens, laying hens; local breeds and wild species). The data are described using metadata techniques and the metadata associated with the animal and its original population. No phenotypic infofmation is shared. The comparison of the sequences belonging to version 5 of the reference genome has allowed the creation of a catalogue containing over 40 million SNP variants. The structural analysis of the populations identified seven genetic groups. The MC1R gene was chosen as an example allowing to detect a signature of selection in laying hens with red feathers. Other candidate genes for shell quality are being studied.

Other data produced in Europe and in China show that 1000 chicken genomes have already been sequenced. The principles for a consortium agreement are being discussed in order to expand our project to a larger number of sequence data.

See also

TIXIER-BOICHARD, M., LECERF, F., HÉRAULT, F., BARDOU, P., & KLOPP, C. (2021). Le projet « Mille Génomes Gallus » : partager les données de séquences pour mieux les utiliser. INRAE Productions Animales, 33(3), 189–202. https://doi.org/10.20870/productions-animales.2020.33.3.4564