A genome-wide association study in a large F2-cross of laying hens reveals novel genomic regions associated with feather pecking and aggressive pecking behavior

Abstract

BackgroundFeather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines. Here, we performed a genome-wide association analysis (GWAS) for feather pecking and aggressive pecking behavior, then combined the results with those from the recent selection signature experiment, and linked them to those obtained from a differential gene expression study.MethodsA large F2 cross of 960 F2 hens was generated using the divergent lines as founders. Hens were phenotyped for feather pecks delivered (FPD), aggressive pecks delivered (APD), and aggressive pecks received (APR). Individuals were genotyped with the Illumina 60K chicken Infinium iSelect chip. After data filtering, 29,376 SNPs remained for analyses. Single-marker GWAS was performed using a Poisson model. The results were combined with those from the selection signature experiment using Fisher’s combined probability test.ResultsNumerous significant SNPs were identified for all traits but with low false discovery rates. Nearly all significant SNPs were located in clusters that spanned a maximum of 3 Mb and included at least two significant SNPs. For FPD, four clusters were identified, which increased to 13 based on the meta-analysis (FPDmeta). Seven clusters were identified for APD and three for APR. Eight genes (of the 750 investigated genes located in the FPDmeta clusters) were significantly differentially-expressed in the brain of hens from both lines. One gene, SLC12A9, and the positional candidate gene for APD, GNG2, may be linked to the monomanine signaling pathway, which is involved in feather pecking and aggressive behavior.ConclusionsCombining the results from the GWAS with those of the selection signature experiment substantially increased the statistical power. The behavioral traits were controlled by many genes with small effects and no single SNP had effects large enough to justify its use in marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0287-4) contains supplementary material, which is available to authorized users.

Genomewide Mapping of Selection Signatures and Genes for Extreme Feather Pecking in Two Divergently Selected Laying Hen Lines

“…Brinker et al [41] found a GABAergic system related candidate gene (GABBR2, Chromosome 2) for direct genetic effects for survival time which is linked to cannibalism in crossbred laying hens. Lutz et al [6] found a candidate gene (SLC12A9) on Chromosome 9 for FPD in a study of a large F2 cross of the HFP and LFP lines. The SCL12 gene family plays a role in the GABAergic system as well.…”

“…Low to medium heritabilities were frequently found [2,3] indicating the possibility to breed for this trait which has also been proven in several selection experiments [4]. A number of mapping studies revealed quantitative trait loci (QTL) and trait-associated genome-regions, but also highlighted the quantitative and complex nature of this trait [5,6], because the few significant QTL by far did not explain the total genetic variance. One approach to identify candidate regions in the genome is to map selection signatures in selected lines.…”

Invited review: Genome-wide association analysis for quantitative traits in livestock – a selective review of statistical models and experimental designs

“…Another way of modeling population structure is to fit principal components (Patterson et al, 2006), but, as Hayes (2013) pointed out, it is not exactly traceable which variation source they actually remove. It may be noted that removing population structure effects is not straightforward when generalized linear models (e.g., Poisson models) are applied (Lutz et al, 2017).…”

Analysis of the source of aggressiveness in gamecocks

“…On the basis of the typical brain monoamine levels, we propose that aggressiveness may be related to the ADR genes based on the observed relative differences in brain NE level. Aggressiveness is determined by several genes and neurotransmitters [70][71][72][73][74][75][76] . Identification of these factors may help elucidate their modes of action.…”