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A genome-wide association study for egg shell strength in the genome of brown-egg layers
Egg shell quality is important for commercial egg production. The objective of this study was to identify single nucleotide polymorphisms (SNPs) that are significantly associated with egg shell strength using either own phenotype or deregressed estimated breeding values (DEBV) in brown-egg laying chickens. In this study egg shell strength data were available for 8,113 purebred line chickens and of which 2,220 had 60k SNP genotype data. Genetic background of shell strength was confirmed by a heritability estimate of 0.29 (SE=0.03) from this data. The number of chickens with both genotypes and phenotype was 650. Three genome wide association analyses (GWAS) were performed. Single SNP regression (SSR) was used to estimate the SNP effects. The first GWAS analysis was performed on 650 chickens and the model for SSR used own phenotype as the response variable and identified no significant associations (FDR≤0.05). To increase the statistical power, DEBV, with their weights, were used as the response variable for two additional association analyses. Chickens with reliabilities of DEBV less than 0.05 were removed from the data set, resulting in 1,429 chickens and 36,103 SNPs. In the second GWAS study we found two significant SNP (FDR ≤ 0.05) associated with egg shell strength on GGA1 and GGA2. The third GWAS analysis was carried out with a more stringent data filtering, only chickens with reliabilities of DEBV greater than 0.08 were kept (N = 1,147). With the more stringent filtering no significant SNP associations were found (FDR≤0.05). Less stringent data filtering can lead to more significant results probably due to higher power from including more animals, but could also indicate false positive results from including unreliable data points. In addition, GWAS analysis with DEBV as phenotypes may not be a simple solution that works well in any species. The utility of DEBV for GWAS in chickens may be smaller because more information comes from half and full sib families in comparison to for instance cattle.
Keywords: Egg shell strength; GWAS; Deregression