The "One Thousand Gallus Genomes" project: sharing sequence data for better use.

Whole genome sequencing has become affordable in hens. The aim of the "One Thousand Gallus Genomes" project is to collect sequences from animals of the genus Gallus produced in research projects. The aim is to increase the power of genomic analysis by increasing the number of genomes compared. Possible applications include the analysis of genome structure, the overall characterization of species diversity, the identification of causal mutations and assistance in genomic selection.
This synthesis first describes the context of hen genomics before developing the concept of "One Thousand Genomes", illustrating it with a pilot project carried out by French teams and discussing the modalities of its extension.
The French pilot project brings together 207 individual sequences for 8 publicly funded research projects on a wide range of populations (broilers, layers, local breeds, wildlife). The datasets are described by technical metadata and metadata related to the animal and its population of origin. No phenotypic information is shared. Comparison of sequences to version 5 of the reference genome has resulted in the identification of more than 40 million SNP variants. The population structure analysis identified seven genetic groups. The MC1R gene was chosen as an example to detect a selection signature in red plumage layers and other candidate genes are being studied for shell quality.
Other data produced in Europe and China show that 1000 chicken genomes have already been sequenced. The principles of a consortium agreement are outlined in order to extend our project to more sequence data.