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.

附加文件1：表S1 本研究中聚合酶链式反应（PCR）所用引物及退火温度。表S2 DKK2基因的短发卡RNA（shRNA）/小干扰RNA（siRNA）靶位点。表S3 4个猪品种的群体规模与重测序深度。表S4 55个重测序样本及12个下载样本的质量控制、比对率与覆盖深度。表S5 单核苷酸多态性（SNP）检测与注释结果。表S6 各群体常见单核苷酸变异（SNV）统计数据。表S7 推定祖先群体的交叉验证误差对应值。表S8 沙子岭猪特有的受选择候选基因。表S9 沙子岭猪特有受选择基因的基因本体（GO）分子功能（MF）分析结果。表S10 沙子岭猪特有受选择基因的京都基因与基因组百科全书（KEGG）通路分析结果。表S11 基于S-BS-BS的血缘同一性（IBD）分析。表S12 基于S-BS-DBS的IBD分析候选基因的GO富集分析结果。表S13 基于S-BS-DBS的IBD分析候选基因的KEGG富集分析结果。表S14 用于DKK2基因选择性清除分析的下载个体重测序数据。表S15 沙子岭猪与其他中国地方猪品种的选择性清除分析结果。表S16 外国猪品种与中国地方猪品种的选择性清除分析结果。表S17 大芭沙杂交品系的表型性状数据。表S18 DKK2基因的SNP变异。