Changing scale in the molecular approach of chicken domestication by undertaking whole genome resequencing for several species is the major ambition of this project. Little is known of the history of chicken domestication at the genome level, in particular the relation with wild species of the genus Gallus. The project involves the four wild species of the genus Gallus: Gallus gallus (red junglefowl), Gallus sonneratii (grey junglefowl), Gallus varius (green junglefowl) and Gallus lafayetii (Sri Lanka junglefowl) and an outgroup species, Bambusicola thoracicus (Chinese bamboo-partridge) known as a sister group of the genus Gallus. The project will use genome sequencing to analyze with an unprecedented resolution the structure of genetic diversity within the genus Gallus, to better understand the make-up of the genome of domestic chickens and to propose molecular tools for the management of wild populations in zoological gardens. Several events of domestication have most probably taken place and a few studies showed that two species, at least, of the genus Gallus could be involved (Gallus gallus and Gallus sonneratii). Our preliminary data suggest that more than 20 regions could have been introgressed from G. sonneratii or G. lafayetii. The identification of such introgression phenomena has a fundamental interest in order to understand to what extent the current structure of the genome of domestic chicken reflects a complex process of domestication. Furthermore, introgression may have involved regions controlling traits of high selective value for breeders. Practical consequences for the management of populations in areas where wild junglefowls and domestic chickens cohabit are expected. A large scale sampling will be undertaken to obtain DNA from genuine wild junglefowls, the absence of recent crossbreeding will be checked with a 60K SNP chip. An array of domestic chickens from different breeds will be sampled to maximise genetic diversity. Sequencing with a very high coverage (95X) will be performed for Bambusicola thoracicus and resequencing with a high coverage (20X) will be done for 48 wild Gallus and 24 domestic chickens. Sequence fragments will be aligned on the reference Gallus gallus sequence. The evolutionary dynamics at the genus level will be addressed with Approximate Bayesian Computation by Population Monte Carlo (ABC-PMC) to uncover qualitative aspects of the complex events (mutations, incomplete lineage sorting, lateral gene transfers...) which shaped the dynamics of the Gallus genus. Footprints left by all types of selection will be searched on coding sequences and non-coding sequences (using outlier approaches based on the XP-EHH score) to increase our understanding of the evolutionary dynamics at play both within the genus during evolutionary timescales and within the domesticated species. We will refine and adapt to the domestic chicken a methodology recently developed to investigate the evolutionary relationships between Neandertals and present-day humans. The local ancestry of domestic chickens along the genome will be modelled with a hidden process. The trajectory of such a process naturally segments the genome and indicates for each segment from which Gallus species it is most likely to derive. Variation in linkage disequilibrium among domestic chickens will be assessed at the same time. A wealth of new sequencing information will be obtained that will be made available for follow-up studies. Annotations of genes in the introgressed regions will also open the way to follow-up functional studies. A specific workshop dedicated to the genomics of domestication will be organised with invited experts working on similar issues in other species. This project will significantly contribute to the international initiative on avian genomes as well as to the 10K vertebrate genomes initiative.