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Human driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg laying chicken along with pool sequences of three meat type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or pre-improvement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in 'Ascites' in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement of chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to over-consumption of calcium in egg laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders. Open-Access Publikationsfonds 2015 peerReviewed

In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a “creeping window” strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value

International audience

Traditional battery cages for laying hens will soon be banned in the EU but the increased risk of feather pecking (FP) hampers the adoption of alternative housing systems. FP can cause injury and lead to cannibalism and the painful death of target birds. Current management practices (beak trimming, low light) have associated problems. In a joint European project we sought alternative solutions. In our study of associated traits, birds from a line showing low (LFP) rather than high feather pecking (HFP) exhibited greater sociality (motivation to be near companions) and a passive 'coping' style. High sociality and passivity were also negatively associated with FP in adults. These findings may guide future breeding programs. Trimming hens' feathers to mimic the results of FP elicited pecking and some cannibalism, even by birds that had previously shown no FP. Social transmission of gentle but not severe FP occurred when LFP and HFP birds were housed together. Gentle pecking could conceivably lead to severe FP. We then examined chickens' pecking preferences to guide environmental enrichment strategies. Bunches of string elicited substantially greater interest than other stimuli, including feathers, and white or yellow string was the most attractive. The birds' manipulation of the string resembled preening. Incorporating silver beads or moving the devices reduced pecking. String sustained lengthy interest, reduced FP in HFP birds, and decreased feather damage in caged layers on a commercial farm. String offers effective, affordable and practicable environmental enrichment. The integrated application of appropriate environmental and genetic strategies is likely to attenuate the expression of FP and its harmful consequences.