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

Abstract

Feather pecking (FP) is a longstanding serious problem in commercial flocks of laying hens. It is a highly polygenic trait and the genetic background is still not completely understood. In order to find genomic regions influencing FP, selection signatures between laying hen lines divergently selected for high and low feather pecking were mapped using the intra-population iHS and the inter-population F_ST approach. In addition, the existence of an extreme subgroup of FP hens (EFP) across both selected lines has been demonstrated by fitting a mixture of negative binomial distributions to the data and calculating the posterior probability of belonging to the extreme subgroup (pEFP) for each hen. A genomewide association study (GWAS) was performed for the traits pEFP and FP delivered (FPD) with a subsequent post GWAS analysis. Mapping of selection signatures revealed no clear regions under selection. GWAS revealed a region on Chromosome 1, where the existence of a QTL influencing FP is likely. The candidate genes found in this region are a part of the GABAergic system, which has already been linked to FP in previous studies. Despite the polygenic nature of FP, selection on these candidate genes may reduce FP.

Keywords: QTL; divergent selection; extreme feather pecking; laying hens; selection signatures.

Figure 1

Multidimensional scaling of the high (HFP, n = 272) and low (LFP, n = 222) feather pecking lines. The distance to each other visualize their genetic distance.

Figure 2

Histogram of feather pecks delivered in bouts per bird (bpb) for (a) the high (HFP, n = 270) and (b) low (LFP, n = 222) feather pecking lines. Note the different scales used for clarity.

Figure 3

P-values of the integrated haplotype score (iHS) for (a) the high feather pecking line (HFP, n_SNP = 22,425), (b) the low feather pecking line (LFP, n_SNP = 23,084) and (c) their combination (n_SNP = 16,766). The dashed lines indicate the nominal level of significance p ≤ 10⁻⁵.

Figure 4

(a) Manhattan plot of F_ST-indices (n_SNP = 29,020). The top line indicates the nominal level of significance p_nominal ≤ 5 × 10⁻⁵ and the bottom line the nominal level of significance p_nominal ≤ 5 × 10⁻⁴. (b) Manhattan plot of the −log₁₀ p-values of the combination of the combined iHS p-values and the F_ST p-values (n_SNP = 16,766). The line indicates the nominal level of significance p ≤ 10⁻⁵.

Figure 5

Mixture of negative binomial distribution (black lines) fitted to the feather pecking data (grey bars) in bouts per bird (bpb) of the high and low feather pecking hens (n = 492). The dotted line represents the fit of the feather pecking (FP) subgroup, the dot-dashed line represents the extreme feather pecking (EFP) subgroup and the solid line represents the combination of both and visualizes the good of fit of the mixture distributions.

Figure 6

Manhattan plots of the −log₁₀ p-values for association of SNPs (n_SNP = 28,525) for (a) the posterior probability of extreme feather pecking (pEFP) and (b) feather pecks delivered (FPD). The line indicates the nominal level of significance p ≤ 5 × 10⁻⁵.