Genome-wide association studies on body-weight and body-size traits among Zhedong white geese based on a modified genotyping-by-sequencing method

LCORL is a crucial gene that regulates body weight and size in several organisms, including the graylag geese (Anser anser). However, the effect of this gene in swan geese (Anser cygnoides) has been deemed negligible. As various indigenous goose breeds (A. cygnoides) are systemically selected for their growth performance, a comprehensive understanding of the genetic basis of growth performance-related traits is imperative for goose breeding. A goose double-digest genotyping-by-sequencing (ddGBS) protocol was established by implementing dual restriction enzyme (EcoRI and BfaI) digestion of genomic DNA, followed by the ligation of adapters with paired-end index sequences. The ddGBS method was used to perform genome-wide association studies on body weight in Zhedong white goose, with the aim to identify candidate genes. The novel genome-wide genotyping method detected > 100 K bi-allelic markers per sample and exhibited a high genotyping accuracy demonstrated by the Sanger sequencing method. Moreover, this strategy was used to conduct a longitudinal genome-wide association study (GWAS) on body-weight traits (0–10 weeks), which identified 19 significant loci. These loci exerted significant effects on body weight, but could only explain a small proportion of the phenotypic variation (≤ 0.51%). Nine candidate genes, including growth-related genes (e.g., THADA), were identified in the proximity of significant GWAS markers. The GBS-based GWAS on body size detected candidate variants associated with shank circumference. Each of the four significant single-nucleotide polymorphisms explained 0.57%–0.58% of the phenotypic variance. Furthermore, screening analyses of genomic selection signals between high- and low-body-weight groups at 10 weeks of age detected 754 potential loci under selection. However, no extremely divergent regions were identified in the genome. The modified goose ddGBS approach provided an alternative genotyping workflow for geese, facilitating GWAS on quantitative traits. The preliminary findings of this study revealed that several genetic loci with minor effects, rather than single major genes, regulated body-weight and body-size traits in Zhedong white goose. Furthermore, short-term artificial selection pressure on body-weight traits could improve phenotypes. However, it mildly reshaped the genome on a large scale.