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. 2020 Oct 1;21(1):114.
doi: 10.1186/s12863-020-00920-9.

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

Clemens Falker-Gieske  1 , Hanna Iffland  2 , Siegfried Preuß  2 , Werner Bessei  2 , Cord Drögemüller  3 , Jörn Bennewitz  2 , Jens Tetens  4   5
Affiliations

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

Clemens Falker-Gieske et al. BMC Genet. .

Abstract

Background: Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic variants and affected genes that lead to FP behavior. To achieve that we imputed low-density genotypes from two different populations of layers divergently selected for FP to sequence level by performing whole genome sequencing on founder and half-sib individuals. In order to decipher the genetic structure of FP, genome wide association studies and meta-analyses of two resource populations were carried out by focusing on the traits 'feather pecks delivered' (FPD) and the 'posterior probability of a hen to belong to the extreme feather pecking subgroup' (pEFP).

Results: In this meta-analysis, we discovered numerous genes that are affected by polymorphisms significantly associated with the trait FPD. Among them SPATS2L, ZEB2, KCHN8, and MRPL13 which have been previously connected to psychiatric disorders with the latter two being responsive to nicotine treatment. Gene set enrichment analysis revealed that phosphatidylinositol signaling is affected by genes identified in the GWAS and that the Golgi apparatus as well as brain structure may be involved in the development of a FP phenotype. Further, we were able to validate a previously discovered QTL for the trait pEFP on GGA1, which contains variants affecting NIPA1, KIAA1211L, AFF3, and TSGA10.

Conclusions: We provide evidence for the involvement of numerous genes in the propensity to exhibit FP behavior that could aid in the selection against this unwanted trait. Furthermore, we identified variants that are involved in phosphatidylinositol signaling, Golgi metabolism and cell structure and therefore propose changes in brain structure to be an influential factor in FP, as already described in human neuropsychiatric disorders.

Keywords: Chicken; Feather pecking; Genome wide association study; Imputation; Meta-analysis; Whole genome sequencing.

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Conflict of interest statement

Jens Tetens is associate Editor of BMC Genetics.

Figures

Fig. 1
Fig. 1
Manhattan plots of the meta-analyses of genome wide associations studies from two resource populations (F2 and HS; half-sib) with the phenotypes (a) feather pecks delivered’ (FPD) and (b) the ‘posterior probability of a hen to belong to the extreme feather pecking subgroup’ (pEFP)
Fig. 2
Fig. 2
Enriched GO cellular components terms for genes that contain variants with -log10(p) > 5 that were discovered in the meta-analysis of two genome wide associations studies for the trait ‘feather pecks delivered’ (FPD)
Fig. 3
Fig. 3
Protein interaction map of genes affected by variants (−log10(p) > 5) from the genome wide associations studies meta-analysis with the trait ‘feather pecks delivered’ (FPD)
Fig. 4
Fig. 4
Analysis workflow from raw data to genome wide associations studies meta-analysis results. High coverage whole-genome sequencing (WGS) variants from an F2-cross and a half-sib (HS) population were used as a reference population for the imputation of low-density single nucleotide polymorphism (SNP) chip genotypes
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