Additional file 1 of Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs

Additional file 1: Table S1. Primers and annealing temperatures used for PCRs in this research. Table S2. shRNA/siRNA target site of DKK2 gene. Table S3. Population size and resequencing depth of four pig breeds. Table S4. Quality control, mapping rate and coverage depth of 55 resequenced samples and 12 downloaded samples. Table S5. Results of SNP calling and annotation. Table S6. Statistics of common SNVs in each population. Table S7. Corresponding cross-validation error of presumed ancestral population. Table S8. Shaziling pigs' unique selected candidate genes. Table S9. GO (MF) analysis of S unique selected genes. Table S10. KEGG pathway analysis of S unique selected genes. Table S11. IBD analysis via S-BS-BS. Table S12. GO enrichment of candidate genes of IBD analysis via S-BS-DBS. Table S13. KEGG enrichment of candidate genes of IBD analysis via S-BS-DBS. Table S14. Resequencing data of downloaded Individuals for DKK2 selective swwep analysis. Table S15. Selective sweep analysis of Shaziling pigs and other Chinese local pigs. Table S16. Selective sweep analysis of foerign pigs and Chinese local pigs. Table S17. Phenotypic traits data of Dabasha crossbred line. Table S18. SNP varitation of DKK2 gene.