Abstract
BackgroundCannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Previous studies analysed repeated binomial survival, instead of survival time, which improved accuracies of breeding value predictions. Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival.MethodsSurvival data of three layer crosses (W1 * WA, W1 * WB, and W1 * WC) were used. Each individual had one survival time record and 13 monthly survival (0/1) records. Approximately 30,000 single nucleotide polymorphisms (SNPs) were included in the genome-wide association study (GWAS), using a linear mixed model for survival time, a linear mixed model and a generalized linear mixed model for repeated binomial survival (0/1). Backwards elimination was used to determine phenotypic and genetic variance explained by SNPs.ResultsThe same quantitative trait loci were identified with all models. A SNP associated with DGE was found in cross W1 * WA, with an allele substitution effect of 22 days. This SNP explained 3% of the phenotypic variance, and 36% of the total genetic variance. Four SNPs associated with DGE were found in cross W1 * WB, with effects ranging from 16 to 35 days. These SNPs explained 1 to 6% of the phenotypic variance and 9 to 44% of the total genetic variance. Our results suggest a link of DGE and IGE for survival time in layers with the gamma-aminobutyric acid (GABA) system, since a SNP located near a gene for a GABA receptor was associated with DGE and with IGE (not significant).ConclusionsThis is one of the first large studies investigating the genetic architecture of a socially-affected trait. The power to detect SNP associations was relatively low and thus we expect that many effects on DGE and IGE remained undetected. Yet, GWAS results revealed SNPs with large DGE and a link of DGE and IGE for survival time in layers with the GABAergic system, which supports existing evidence for the involvement of GABA in the development of abnormal behaviors.
Highlights
Cannibalism is an important welfare problem in the layer industry
Variance components from RMM.t and generalized linear mixed model (GLMM) are not presented in Table 2 because they can be translated to the survival time scale, for which estimates are in Table 2 [10]
There were no evident differences between genome-wide association study (GWAS) results from survival time (STM), RMM.t, and GLMM (Tables 3, 4) and [see Additional files 1, 2 and 3]
Summary
Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Our study aimed at identifying SNPs associated with DGE and IGE for survival time, and comparing results from models that analyse survival time and repeated binomial survival. Mortality due to cannibalism has important welfare and economic implications in the commercial laying hen industry. Previous research revealed that survival time is affected both by an individual’s own genes (direct genetic effects; DGE) and by genes of its group mates (indirect genetic effects; IGE). It was found that IGE contribute 33 to 76% of the heritable variation in survival time in purebred and crossbred laying hens with intact beaks [2, 3]. The genetic architecture of survival time in laying hens that show cannibalism remains largely unknown
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