Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens

Abstract

Egg weight (EW) is an economically-important trait and displays a consecutive increase with the hen's age. Because extremely large eggs cause a range of problems in the poultry industry, we performed a genome-wide association study (GWAS) in order to identify genomic variations that are associated with EW. We utilized the Affymetrix 600 K high density SNP array in a population of 1,078 hens at seven time points from day at first egg to 80 weeks age (EW80). Results reveal that a 90 Kb genomic region (169.42 Mb ~ 169.51 Mb) in GGA1 is significantly associated with EW36 and is also potentially associated with egg weight at 28, 56, and 66 week of age. The leading SNP could account for 3.66% of the phenotypic variation, while two promising genes (DLEU7 and MIR15A) can be mapped to this narrow significant region and may affect EW in a pleiotropic manner. In addition, one gene (CECR2 on GGA1) and two genes (MEIS1 and SPRED2 on GGA3), which involved in the processes of embryogenesis and organogenesis, were also considered to be candidates related to first egg weight (FEW) and EW56, respectively. Findings in our study could provide worthy theoretical basis to generate eggs of ideal size based on marker assisted breeding selection.

Functional and whole regression-based genome-wide association analyses for weight measurements of chicken eggs

“…Liu et al [14] detected the genomic signal specifically for week 36 and our fGWAS data (when combining whole longitudinal observations) confirmed this result. However, Liu et al [14] stated that the associated signals of chromosome 1 for week 36 also correlated with weeks 28, 56, and 66, but without reaching statistical significance.…”

“…Using fGWAS, we mapped the associated region ( Figure 3) previously shown to include a QTL affecting the EW on chromosome 1 [14]. Liu et al [14] detected the genomic signal specifically for week 36 and our fGWAS data (when combining whole longitudinal observations) confirmed this result.…”

“…The results obtained from this study show that fGWAS can be useful for manipulating dynamic EW over the entire laying period (based on a moderate to major effect). The fGWAS SNPs that were associated with EW were located on chromosome 1, close to the gene DLEU7, which regulates ovary weight in chickens [14,33]. The SNPs were detected based on the absolute effect sizes using Bayes C(π) ( Table 5) and BL (Table 6) is likely useful for predicting the polygenic risk scores and/or genomic breeding values during genomic selection for longitudinal EW measurements.…”

“…Recently, Liu et al [14] detected time specific genomic signals for EW using separate association tests. The main objective of this study is to predict the genomic signals over a logistic curve referring to multiple underlying genetic architectures, for both simulated [15] and longitudinal EW [14] datasets.…”

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

“…Sichuan White is a popular Chinese goose breed reared for both meat and eggs. While egg laying and egg quality traits have been studied intensively in avians, including chickens [29,30], ducks [15,31], and quail [32], few studies have examined traits other than those associated with egg laying in the goose genome [13].…”