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

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.

The light response in chickens divergently selected for feather pecking behavior reveals mechanistic insights towards psychiatric disorders

“…Due to the low number of DEGs in HFP no gene cluster analysis could be performed. To identify genetic variation that might explain the strong difference between the two chicken lines a previously performed genome-wide association study (GWAS) [ 4 ] was repeated with a modified phenotype: feather pecks delivered box-cox transformed (Fig. 1 e, Supplementary Information S3).…”

“…Upon initiation of FP behavior these birds we sacrificed as well and brains were collected for RNA isolation. For the detection of genetic variation between the two chicken lines animals were phenotyped in groups of 42 hens at the age of 32 weeks and observed in 20 min sessions by seven independent trained observers [ 4 ]. Phenotypic values were standardized to 420 min observation time followed by box-cox transformation as described by Iffland et al [ 8 ].…”

“…Phenotypic values were standardized to 420 min observation time followed by box-cox transformation as described by Iffland et al [ 8 ]. Analysis pipelines of transcriptomic and genomic data are outlined in our previous studies [ 3 , 4 ]. Briefly, Illumina short RNA sequencing reads were trimmed and filtered with trimmomatic, mapped to the chicken reference assembly GRCg6a with TopHat, differential expression analysis was performed with DEseq2, and gene set enrichment analysis with clusterProfiler.…”

“…Common features with obsessive compulsive disorder like involvement of immune mechanisms have been reported [ 2 ]. Furthermore, in previous studies, we identified putative enhancer RNAs that target schizophrenia-associated genes [ 3 ] as well as numerous genetic variants in genes that have been previously linked to schizophrenia, namely GABRB2 , SPATS2L , ZEB2 , and KCHN8 [ 4 ]. Hence, FP may be a potential model system for these conditions.…”

The Prevalence of Integument Injuries and Associated Risk Factors Among Canadian Turkeys

“…Aggressive pecking targets the head, neck, and snood areas in turkeys (3)(4)(5) and tends to be related to establishing/maintaining social hierarchy (6,7), although it can escalate into violence with no apparent function (5). Severe feather pecking is suggested to be a redirected foraging behavior, possibly from frustration due to a lack of environmental enrichment ["ethological view": (1,7) or, alternatively, a result of changes in brain structure similar to neuropsychiatric disorders ["dysfunctional view": (1,8)]. Typically, this behavior targets the wings, back, and/or tail, and pecking bouts can cause substantial feather loss (2,3).…”