Additional file 2 of Genome‑wide association study and genomic prediction for growth traits in yellow-plumage chicken using genotyping-by-sequencing

Additional file 2: Table S1. Information on the significant SNPs associated with 42 DW in the QTL region on chromosome 4. The data present the genomic location, effect, heritability, P value, and functional annotation of each GWAS significant SNP associated with 42 DW on chromosome 4. Table S2. Information on the significant SNPs associated with 84 DW in the QTL region on chromosome 4. The data present the genomic location, effect, heritability, P value, and functional annotation of each GWAS significant SNP associated with 84 DW on chromosome 4. Table S3. Information on the significant SNPs associated with ADG in the QTL region on chromosome 4. The data present the genomic location, effect, heritability, P value, and functional annotation of each GWAS significant SNP associated with ADG on chromosome 4. Table S4. Information on the significant SNPs associated with FCR in the QTL region on chromosome 4. The data present the genomic location, effect, heritability, P value, and functional annotation of each GWAS significant SNP associated with FCR on chromosome 4. Table S5. Average prediction inflation based on tenfold cross-validation. The data provide the average prediction inflation using ABLUP, GBLUP or GFBLUP models. Table S6. QTL contributions to the theoretical prediction accuracy (%). Description: The contributions were estimated by setting GWAS significant SNPs in each QTL as fixed factors. Table S7. Average prediction inflation addition after setting GWAS significant SNPs as fixed factors. The average prediction inflation changes after setting GWAS significant SNPs as fixed factors, where values approaching 0 represent lower inflations. Table S8. QTL contributions to heritability and observed prediction accuracy (%) using the GFBLUP model. The contributions were evaluated by estimating the contribution of two GRM using the GFBLUP model. Table S9. Average theoretical prediction accuracy using two GRM in the GFBLUP model. The data provide the average theoretical accuracy of prediction based on the GRM of GWAS significant sites and the remaining sites, respectively. Table S10. Average prediction inflation addition in the GFBLUP model. The changes in average prediction inflation evaluated by using the GRM without GWAS significant SNPs compared to that using both GRM, where values approaching 0 represent lower inflations.