The “1000 Gallus Genomes” project: sharing sequence data to better exploit them

Abstract

The 1000 Gallus Genomes project aims at gathering whole genome sequence data in chicken, produced by research projects. It allows increasing the power of analyses by increasing the number of genomes compared. Potential applications target a better knowledge of the chicken genome and of the genetic diversity of the species, the identification of causal mutations and a support to genomic selection. A pilot project has started in France with 207 individual genome sequences produced by eight publicly funded projects on a range of chicken populations (broilers, layers, local breeds, wild ancestors). Datasets are described by metadata for technical parameters, for the animal and its population of origin. Phenotypic data are not shared. Sequences have been compared to version 5 of the reference genome with a common pipeline that identified more than 40 millions SNP variants. A structure analysis led to group the 207 individuals in seven genetic clusters. The MC1R gene was chosen as an example showing how to detect a selection signature related to red plumage in brown-egg layers. Candidate genes for egg-shell quality are under study. Other data produced in Europe and China show that 1,000 chicken genomes have already been sequenced. The principles of a consortium agreement are presented in order to extend our project to a larger set of sequence data.