ORIGINAL RESEARCH Across-Line SNP Association Study for Direct and Associative Effects on Feather Damage in Laying Hens F. Biscarini • H. Bovenhuis • J. van der Poel • T. B. Rodenburg • A. P. Jungerius • J. A. M. van Arendonk Received: 27 January 2010 / Accepted: 7 May 2010 / Published online: 23 May 2010 Ó Springer Science+Business Media, LLC 2010 Abstract An association study between SNP markers and feather condition score on the back, rump and belly of laying hens was performed. Feather condition score is a measure of feather damage, which has been shown to be closely related to feather pecking behaviour in hens housed in groups. A population of 662 hens was genotyped for 1536 SNPs of which 1022 could be used for the association study. The analysis was conducted across 9 different lines of White Leghorn and Rhode Island Red origin. Across lines linkage disequilibrium is conserved at shorter dis- tances than within lines; therefore, SNPs significantly associated with feather condition score across lines are expected to be closer to the functional mutations. The SNPs that had a significant across-line effect but did not show significant SNP-by-line interaction were identified, to test that the association was consistent across lines. Both the direct effect of the individual’s genotype on its plumage condition, and the associative effect of the genotype of the cage mates on the individual’s plumage condition were analysed. The direct genetic effect can be considered as the susceptibility to be pecked at, whereas the associative genetic effect can be interpreted as the propensity to per- form feather pecking. Finally, 11 significant associations between SNPs and behavioural traits were detected in the direct model, and 81 in the associative model. A role of the gene for the serotonin receptor 2C (HTR2C) on chromo- some 4 was found. This supports existing evidence of a prominent involvement of the serotonergic system in the modulation of this behavioural disorder in laying hens. The genes for IL9, IL4, CCL4 and NFKB were found to be associated to plumage condition, revealing relationships between the immune system and behaviour. Keywords Feather pecking  Plumage condition  Association study  SNPs  Laying hens  Direct and associative effects Introduction Feather pecking (FP) is one of the most serious behavioural disorders of laying hens. Severe FP, the type of pecking that causes most feather damage, consists of the forceful pecking and pulling of feathers of other birds (Savory 1995). FP is a multifactorial problem caused by both genetic and envi- ronmental factors. There is evidence of line differences in FP (Kjaer et al. 2001; Uitdehaag et al. 2008), and it has been demonstrated that FP is influenced by group size, light intensity, diet and type of litter (Hughes and Duncan 1972; Blokhuis and Arkes 1984; Savory 1995). As for its aetiol- ogy, FP has been considered to be redirected ground pecking (Blokhuis 1986), abnormal dustbathing behaviour (Vest- ergaard and Lisborg 1993), or the consequence of a more general hyperactivity disorder (Kjaer 2009). Most of the evidence point at the redirected ground pecking theory (Huber-Eicher and Wechsler 1997), with active or even hyperactive birds having the highest risk of developing FP (Newberry et al. 2007; Kjaer 2009). The serotonergic system has been shown to play an important role in the modulation of FP (van Hierden et al. 2002, 2004a, b; Buitenhuis et al. Edited by Stephen Clark Maxson. F. Biscarini (&)  H. Bovenhuis  J. van der Poel  T. B. Rodenburg  J. A. M. van Arendonk Animal Breeding and Genomics Centre, Wageningen University, P.O. Box 338, 6700 AH Wageningen, The Netherlands e-mail: filippo.biscarini@wur.nl A. P. Jungerius Hendrix Genetics, Boxmeer, The Netherlands 123 Behav Genet (2010) 40:715–727 DOI 10.1007/s10519-010-9370-0