Identification of Molecular Markers Associated with Goose Egg Quality Through Genome-Wide Association Analysis

The objective of this study was to screen molecular markers and candidate genes related to goose egg quality traits, to provide a theoretical support for the analysis of the genetic mechanism of egg quality traits and marker-assisted selection.

In this study, a batch of healthy Sichuan White Geese (209 individuals) was selected as the research subjects. Five eggs from each goose during the peak egg production period were collected, and then six egg quality traits were measured, including egg weight, egg shape index, eggshell strength, eggshell thickness, eggshell weight, and egg yolk weight. Based on the whole-genome resequencing data (2.896 Tb, 12.44×/individual) of 209 Sichuan White Geese (female geese), a genome-wide association analysis was conducted to identify SNP loci and important candidate genes associated with egg quality traits. The genotype frequencies of the SNP loci were determined using the nucleic acid flight time mass spectrometry method.

After filtering, a total of 9 279 339 SNPs and 209 individuals were included for further analysis. The GWAS analysis identified 48 SNP loci significantly or suggestively associated with six egg quality traits (thresholds: 5.43×10^-9 and 1.09×10^-7). These loci were annotated to 27 candidate genes related to egg quality traits, including Pregnancy-associated plasma protein A (PAPPA), Serine/threonine-protein phosphatase 4 regulatory subunit 2 (PP4R2), Ethanolamine phosphotransferase 1 (EPT1), and Glutamate receptor ionotropic, kainate 2 (GRIK2). Among them, the candidate gene PAPPA was involved in protein metabolism and promotes the generation of insulin-like growth factor. Five SNPs within the 11 bp range of PP4R2 were significantly associated with eggshell thickness. Additionally, six SNPs on the GRIK2 gene were significantly associated with yolk weight. GRIK2 and PP4R2 were respectively associated with blood calcium homeostasis and cholesterol metabolism in organisms. Functional enrichment analysis revealed that the candidate genes were mainly annotated to “response to growth factor” (GO:0070848), “intracellular chemical homeostasis” (GO:0055082), “response to hormone” (GO:0009725), and “regulation of monoatomic ion transport” (GO:43269).

The GWAS analysis showed that the PAPPA, GRIK2, ASCC3, and EPT1 are potential functional genes associated with various egg quality traits, such as egg weight, egg yolk weight, and shell strength, providing theoretical references for molecular genetic marker-assisted selection of goose egg quality traits.