Genome-wide association analysis and genetic architecture of egg weight and egg uniformity in layer chickens

The pioneering work by Professor Soller et al., among others, on the use of genetic markers to analyze quantitative traits has provided opportunities to discover their genetic architecture in livestock by identifying quantitative trait loci (QTL). The recent availability of high-density single nucleotide polymorphism (SNP) panels has advanced such studies by capitalizing on population-wide linkage disequilibrium at positions across the genome. In this study, genomic prediction model Bayes-B was used to identify genomic regions associated with the mean and standard deviation of egg weight at three ages in a commercial brown egg layer line. A total of 24,425 segregating SNPs were evaluated simultaneously using over 2900 genotyped individuals or families. The corresponding phenotypic records were represented as individual measurements or family means from full-sib progeny. A novel approach using the posterior distribution of window variances from the Monte Carlo Markov Chain samples was used to describe genetic architecture and to make statistical inferences about regions with the largest effects. A QTL region on chromosome 4 was found to explain a large proportion of the genetic variance for the mean (30%) and standard deviation (up to 16%) of the weight of eggs laid at specific ages. Additional regions with smaller effects on chromosomes 2, 5, 6, 8, 20, 23, 28 and Z showed suggestive associations with mean egg weight and a region on chromosome 13 with the standard deviation of egg weight at 26-28 weeks of age. The genetic architecture of the analyzed traits was characterized by a limited number of genes or genomic regions with large effects and many regions with small polygenic effects. The region on chromosome 4 can be used to improve both the mean and standard deviation of egg weight by marker-assisted selection.