title: Genetic parameters and signatures of selection in two divergent laying hen lines selected for feather pecking behaviour.
abstract: BACKGROUND
  Feather pecking (FP) in laying hens is a well-known and multi-factorial behaviour with a genetic background. In a selection experiment, two lines were developed for 11 generations for high (HFP) and low (LFP) feather pecking, respectively. Starting with the second generation of selection, there was a constant difference in mean number of FP bouts between both lines. We used the data from this experiment to perform a quantitative genetic analysis and to map selection signatures.
  
  
  METHODS
  Pedigree and phenotypic data were available for the last six generations of both lines. Univariate quantitative genetic analyses were conducted using mixed linear and generalized mixed linear models assuming a Poisson distribution. Selection signatures were mapped using 33,228 single nucleotide polymorphisms (SNPs) genotyped on 41 HFP and 34 LFP individuals of generation 11. For each SNP, we estimated Wright's fixation index (FST). We tested the null hypothesis that FST is driven purely by genetic drift against the alternative hypothesis that it is driven by genetic drift and selection.
  
  
  RESULTS
  The mixed linear model failed to analyze the LFP data because of the large number of 0s in the observation vector. The Poisson model fitted the data well and revealed a small but continuous genetic trend in both lines. Most of the 17 genome-wide significant SNPs were located on chromosomes 3 and 4. Thirteen clusters with at least two significant SNPs within an interval of 3 Mb maximum were identified. Two clusters were mapped on chromosomes 3, 4, 8 and 19. Of the 17 genome-wide significant SNPs, 12 were located within the identified clusters. This indicates a non-random distribution of significant SNPs and points to the presence of selection sweeps.
  
  
  CONCLUSIONS
  Data on FP should be analysed using generalised linear mixed models assuming a Poisson distribution, especially if the number of FP bouts is small and the distribution is heavily peaked at 0. The FST-based approach was suitable to map selection signatures that need to be confirmed by linkage or association mapping.
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. vanessa.grams@uni-hohenheim.de.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Grams
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. r.wellmann@uni-hohenheim.de.
authors.forename: Robin
authors.initials: R
authors.lastname: Wellmann
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. siegfried.preuss@uni-hohenheim.de.
authors.forename: Siegfried
authors.initials: S
authors.lastname: Preuß
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. michael.grashorn@uni-hohenheim.de.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Grashorn
authors.affiliation: Institute for Animal Welfare and Animal Husbandry, Friedrich-Loeffler-Institut, Doernbergstrasse 25-27, 29223, Celle, Germany. joergen.kjaer@fli.bund.de.
authors.forename: Jörgen B
authors.initials: JB
authors.lastname: Kjaer
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. werner.bessei@uni-hohenheim.de.
authors.forename: Werner
authors.initials: W
authors.lastname: Bessei
authors.affiliation: Institute of Animal Science, University of Hohenheim, 70593, Stuttgart, Germany. j.bennewitz@uni-hohenheim.de.
authors.forename: Jörn
authors.initials: J
authors.lastname: Bennewitz
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D001522:Behavior, Animal / Q000502:physiology*; D002645:Chickens / Q000145:classification* / Q000235:genetics / Q000502:physiology; D002874:Chromosome Mapping / Q000379:methods; D040961:Genetic Drift; D010375:Pedigree; D016012:Poisson Distribution; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic