Across‐line SNP association study of innate and adaptive immune response in laying hens

Abstract

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in laying hens. For this purpose, the associations between 1022 single nucleotide polymorphism (SNP) markers and immune traits were studied in 583 hens from nine different layer lines. Immune traits were natural antibodies for keyhole limpet haemocyanin (KLH) and lipopolysaccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to the vaccinal virus of Newcastle disease at 20 weeks, and complement activity measured on sheep and bovine red blood cells at 20, 40 and 65 weeks. We adopted a novel approach based on across-line analysis and testing of the SNP-by-line interaction. Among lines, linkage disequilibrium is conserved at shorter distances than in individual lines; therefore, SNPs significantly associated with immune traits across lines are expected to be near the functional mutations. In the analysis, the SNPs that had a significant across-line effect but did not show significant SNP-by-line interaction were identified to test whether the association was consistent in the individual lines. Ultimately, 59 significant associations between SNPs and immune traits were detected. Our results confirmed some previously identified QTL and identified new QTL potentially involved in the immune function. We found evidence for a role of IL17A (chromosome 3) in natural and acquired antibody titres and in the classical and alternative pathways of complement activation. The major histocompatibility genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The IL12B gene on chromosome 13 was associated with natural antibody titres.

Across-Line SNP Association Study for Direct and Associative Effects on Feather Damage in Laying Hens

“…Relations between behaviour and immunity have been suggested also in other works. Biscarini et al (2010) detected associations between the serotonin receptors HTR2C and HTR2A and, respectively, complement activity and antibody titres. Combining their results with the ones of the present study, we see that in the case of HTR2C higher feather damage corresponds to lower complement activity.…”

“…Finally, only 1 SNP (rs15385785) is consistently associated with the phenotype in all lines, and due to the lower extent of LD conserved across all lines, this is likely to be closer to the QTL for the trait. The same procedure was applied by Biscarini et al (2010) in an association study of immune response in laying hens.…”

“…These constitute two subpopulations of different origin (White Leghorn and Rhode Island Red, respectively), both comprising different lines. White and brown layers form two distinct phylogenetic clusters (Biscarini et al 2010), implying that LD patterns are better conserved within than across them (Andreescu et al 2007). When analysing the two subpopulations separately many SNPs result to be significantly associated with the phenotype (BR51): 3 in the white layers and 8 in the brown layers.…”

“…Thus, 1022 SNPs were used in the association study. Details on the SNP editing procedure are described by Biscarini et al (2010).…”

“…We performed an association study between SNP markers and feather condition score across 9 lines of layers of White Leghorn (white feathered) and Rhode Island Red (brown feathered) origin, looking at the interaction between the SNP and line effects (Saccone et al 2008;Biscarini et al 2010). SNPs showing a significant across line association and no SNP-by-line interaction were considered to be consistently associated with the phenotype.…”