Across-line SNP association study for (innate) immune and behavioral traits in laying hens

A population of about 600 hens was genotyped for 1022 SNP for the association study. The analysis was conducted across 9 different lines of White Leghorn and Rhode Island Red origin. Across line linkage disequilibrium is conserved at shorter distances than within lines; therefore, SNP significantly associated with traits across lines are expected to be closer to functional mutations. SNP having a significant across-line effect but no significant SNPby- line interaction were identified, to test for consistency of association across lines. Immune traits were Natural antibodies for keyhole limpet haemocyanin (KLH), lipopoly-saccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to Newcastle disease virus vaccine at 20 weeks, and classical and alternative Complement activity measured at 20, 40 and 65 weeks. Feather condition score on the back, rump and belly of laying hens was performed as a measure of feather damage, which is closely related to feather pecking behavior in group-housed hens. The direct genetic effect (susceptibility to being pecked) and associative effect (propensity to perform pecking) on plumage condition were analyzed. Thus, 11 significant SNP associations were detected in the direct model and 81 in the associative model. The serotonin receptor 2C (HTR2C) gene on chromosome 4 was highlighted, supporting existing evidence of prominent involvement of the serotonergic system in modulation of feather pecking behavior in laying hens. For immune traits 59 significant SNP associations were detected, confirming previously identified QTL and showing unexpected involvement of IL17A (chromosome 3) in natural and acquired antibody titres and Complement cascade activation.