Genetics and genomics of direct and social genetic effects on survival time and plumage condition in laying hens

With social interactions, individuals may affect each other’s phenotype. In these cases, an individual’s phenotype depends on the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its mates (IGE). This thesis focusses on two traits related to cannibalistic interactions among laying hens: plumage condition and survival time. This thesis shows that up to 94% of the heritable variation in plumage condition and up to 61% of the heritable variation in survival time relates to IGE. Thus, genetic selection methods incorporating both DGE and IGE offer perspectives to improve both traits. Shortcomings of studies using DGE-IGE models that focussed on survival time are that censored records were considered as exact lengths of life and models assumed that IGE were continuously expressed by all cage members, even after death. This may reduce accuracy of estimated breeding values (EBV). This thesis showed that the accuracy of EBV for survival time can be improved using models that incorporate censoring. This will also contribute to higher rates of genetic gain. Another tool to improve EBV accuracy could be to use genomic information instead of pedigree information. This thesis showed that using genomic information did not improve the accuracy of EBV for survival time. Genomic information is also used in Genome-Wide Association Studies (GWAS). Only a handful of studies extended GWAS to include IGE. In this thesis, SNPs associated with direct and indirect effects for survival time were identified. GWAS results revealed SNPs with large DGE and a link of DGE and IGE for survival time in laying hens with the GABAergic system. This supports existing evidence for the involvement of GABA in the development of abnormal behaviors. SNP effects can differ among crosses due to different levels of linkage disequilibrium between the SNP and the QTL in the parental lines. If this matters, the power of SNP detection is expected to increase when alleles are mapped specific to their allele origin. This thesis aimed to map DGE and IGE for survival time, while considering the line origin of the alleles. However, accurately assigning the line origin to alleles, appeared to be challenging: new Mendel errors were identified after assigning the line of origin to alleles (additional to the identified Mendel errors based on SNP genotypes). These errors had a large impact on the results of the GWAS analyses. Moreover, it is recommended to repeat the quality control based on Mendel errors after allele origin assignment. Finally, it is discussed that the topic of this thesis is very relevant in the light of sustainable egg production, because i) it addresses important societal concerns, and ii) it contributes to sustainable development goal “End hunger” (SDG2) of the Food and Agricultural Organization of the United Nations.&nbsp