Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Feb 6;10(2):262.
doi: 10.3390/ani10020262.

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

Hanna Iffland  1 , Robin Wellmann  1 , Markus Schmid  1 , Siegfried Preuß  1 , Jens Tetens  2 , Werner Bessei  1 , Jörn Bennewitz  1
Affiliations

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

Hanna Iffland et al. Animals (Basel). .

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 FST 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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
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
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
Figure 3
P-values of the integrated haplotype score (iHS) for (a) the high feather pecking line (HFP, nSNP = 22,425), (b) the low feather pecking line (LFP, nSNP = 23,084) and (c) their combination (nSNP = 16,766). The dashed lines indicate the nominal level of significance p ≤ 10−5.
Figure 4
Figure 4
(a) Manhattan plot of FST-indices (nSNP = 29,020). The top line indicates the nominal level of significance pnominal ≤ 5 × 10−5 and the bottom line the nominal level of significance pnominal ≤ 5 × 10−4. (b) Manhattan plot of the −log10 p-values of the combination of the combined iHS p-values and the FST p-values (nSNP = 16,766). The line indicates the nominal level of significance p ≤ 10−5.
Figure 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
Figure 6
Manhattan plots of the −log10 p-values for association of SNPs (nSNP = 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.
See this image and copyright information in PMC

References

    1. Rodenburg T.B., van Krimpen M.M., de Jong I.C., de Haas E.N., KOPS M.S., Riedstra B.J., Nordquist R.E., Wagenaar J.P., Bestman M., Nicol C.J. The prevention and control of feather pecking in laying hens: Identifying the underlying principles. Worlds Poult. Sci. J. 2013;69:361–374. doi: 10.1017/S0043933913000354. - DOI
    1. Wysocki M., Bessei W., Kjaer J.B., Bennewitz J. Genetic and physiological factors influencing feather pecking in chickens. Worlds Poult. Sci. J. 2010;66:659–672. doi: 10.1017/S0043933910000644. - DOI
    1. Bennewitz J., Bögelein S., Stratz P., Rodehutscord M., Piepho H.P., Kjaer J.B., Bessei W. Genetic parameters for feather pecking and aggressive behavior in a large F2-cross of laying hens using generalized linear mixed models. Poult. Sci. 2014;93:810–817. doi: 10.3382/ps.2013-03638. - DOI - PubMed
    1. Buitenhuis A.J., Kjaer J.B. Long term selection for reduced or increased pecking behaviour in laying hens. Worlds Poult. Sci. J. 2008;64:477–487. doi: 10.1017/S0043933908000159. - DOI
    1. Buitenhuis A.J., Rodenburg T.B., van Hierden Y.M., Siwek M., Cornelissen S.J.B., Nieuwland M.G.B., Crooijmans R.P.M.A., Groenen M.A.M., Koene P., Korte S.M., et al. Mapping Quantitative Trait Loci Affecting Feather Pecking Behavior and Stress Response in Laying Hens. Poult. Sci. 2003;82:1215–1222. doi: 10.1093/ps/82.8.1215. - DOI - PubMed

LinkOut - more resources