Abstract
Geese are one of the most economically important waterfowl. However, the low reproductive performance and egg quality of geese hinder the development of the goose industry. The identification and application of genetic markers may improve the accuracy of beneficial trait selection. To identify the genetic markers associated with goose reproductive performance and egg quality traits, we performed a genome-wide association study (GWAS) for body weight at birth (BBW), the number of eggs at 48 weeks of age (EN48), the number of eggs at 60 weeks of age (EN60) and egg yolk color (EYC). The GWAS acquired 2.896 Tb of raw sequencing data with an average depth of 12.44× and identified 9,279,339 SNPs. The results of GWAS showed that 26 SNPs were significantly associated with BBW, EN48, EN60, and EYC. Moreover, five of these SNPs significantly associated with EN48 and EN60 were in a haplotype block on chromosome 35 from 4,512,855 to 4,541,709 bp, oriented to TMEM161A and another five SNPs significantly correlated to EYC were constructed in haplotype block on chromosome 5 from 21,069,009 to 21,363,580, which annotated by TMEM161A, CALCR, TFPI2, and GLP1R. Those genes were enriched in epidermal growth factor-activated receptor activity, regulation of epidermal growth factor receptor signaling pathway. The SNPs, haplotype markers, and candidate genes identified in this study can be used to improve the accuracy of marker-assisted selection for the reproductive performance and egg quality traits of geese. In addition, the candidate genes significantly associated with these traits may provide a foundation for better understanding the mechanisms underlying reproduction and egg quality in geese.
Highlights
As one of the most economically important waterfowl, geese are widely raised for their eggs, meat, liver, feathers, and other byproducts (Boz et al, 2017)
The body weight (BBW), laying performance (EN48 and the number of eggs at 60 weeks (EN60)), and egg quality (EYC) of all 209 Sichuan white geese were recorded during the laying period (Table 1)
We used a mixed linear model in the genome-wide efficient mixed model association (GEMMA) software package to adjust for variations in population structure and conducted a genomewide association study (GWAS) analysis for the selected traits
Summary
As one of the most economically important waterfowl, geese are widely raised for their eggs, meat, liver, feathers, and other byproducts (Boz et al, 2017). The yolk is rich in various amino acids, fatty acids, vitamins, and minerals, which provide enough nutrition for the developing embryo (Zaheer, 2017; Zhu et al, 2020). The shell is an essential component of the egg, as it provides calcium for embryonic development (Samiullah and Roberts, 2014). Given the importance of goose reproductive performance and egg quality, researchers focused on improving the production and quality of egg of goose (Ouyang et al, 2020; Zhao et al, 2020)
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