Sequence-based Analysis of Selection during Domestication and Improvement of Chicken

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Domestication followed by breed formation and massive selection has likely left detectable signatures in the genome of modern chickens. Since the wild Red Jungle Fowl (RJF, Gallus gallus gallus), the primary progenitor of chicken is still available, a post versus pre-domestication comparison of genomic patterns is possible. This facilitates identifying so-called domestication genes that have been primary targets of selective forces during domestication. It also allows testing the hypothesis that domestication and subsequent breeding has led to relaxation of negative selection on particular genes and pathways. To this purpose, we will re-sequence 30 birds from three populations (one layer line, one broiler line, RJF), respectively. Four major objectives are addressed: (1) we will analyze the genome-wide pattern of demographic history to infer major evolutionary switches, (2) we will test for evidence of cases where negative selection on functional processes has been relaxed during domestication or formation of breeding lines (3) we will construct a high-resolution map of signatures left by positive selection, and (4) we will unravel the extent to which balancing selection has influenced chicken genome variability. We will employ cutting edge methodologies and extensive simulations in collaboration with some pioneering labs in the field of population genomics. The novelties are three fold: First, re-sequencing individual birds on a population scale provides the full data profile of each individual (e.g., allelic, genotypic and haplotypic states) that were not available genome-wide so far. This allows genomic scans with highest resolution and fairly free of ascertainment bias, and results can be validated across multiple methods and/or sources of information. Second, a sizable population of RJF will be sequenced that can be used to verify, correct and where necessary extend the reference sequence, improving the basis for any future population based studies of chicken genome. Third, this project takes first steps towards unraveling footprints left by adaptive forces other than positive selection (e.g. relaxed negative and balancing selection) in the chicken genome. The expected results will substantially advance our knowledge of adaptive biology and will contribute to an in-depth understanding of the processes underlying domestication and subsequent human-driven breed formation of modern chickens as a model for farm animal domestication.