Fig. 7
PAV-GWAS and gene frequencies between geese breeds. A Manhattan plot of gene PAV-GWAS for shell genes located outside the reference genome. The analysis was conducted for eight different phenotypes, and significantly associated genes were labeled with the abbreviations of proteins as follows: RCVRN: Recoverin, FOXRED1: FAD-dependent oxidoreductase domain-containing protein 1, RPL18: Large subunit ribosomal protein L18e, MKK7: Mitogen-activated protein kinase kinase 7, NIT1: Nitrilase homolog 1, GANAB: Mannosyl-oligosaccharide alpha-1,3-glucosidase, and PDE4: cAMP-specific phosphodiesterase 4. B Comparison analysis of gene frequencies between domestic geese in China and domestic geese in Europe, as well as GO enrichment analysis results of genes with frequency differences. The domestic geese from China include Sichuan white goose, Huoyan goose, Xupu goose, Zi goose, Magang goose, Lion head goose, and Taihu goose, while the domestic geese from Europe include White Roman goose and Landes goose. C Comparison analysis of gene frequencies between domestic geese in China and wild geese, as well as GO enrichment analysis results of genes with frequency differences. The wild geese species include Bar-headed goose, Barnacle goose, Black Brent goose, Cackling goose, Dark-bellied Brent goose, Emperor goose, Greater White-fronted goose, Greylag goose, Lesser White-fronted goose, Pink-footed goose, Red-breasted goose, Wan goose, Taiga Bean goose, and Tundra Bean goose. D Comparison analysis of gene frequencies between domestic geese in Europe and wild geese, as well as GO enrichment analysis results of genes with frequency differences. E Comparison analysis of gene frequencies between domestic geese with high body weight and medium body weight, as well as GO enrichment analysis results of genes with frequency differences. The breeds with medium body weight include Sichuan white goose and Xupu goose. F Comparison analysis of gene frequencies between domestic geese with high body weight and low body weight, as well as GO enrichment analysis results of genes with frequency differences. G Comparison analysis of gene frequencies between domestic geese with high-reproductive-ability and low-reproductive-ability, as well as GO enrichment analysis results of genes with frequency differences. H Comparison analysis of gene frequencies between domestic geese with medium-reproductive-ability and low-reproductive-ability, as well as GO enrichment analysis results of genes with frequency differences. The breeds with medium-reproductive-ability include Taihu goose and Sichuan white goose. The threshold for significantly different gene frequencies was set at a fold change > 2 and Padj < 0.001