Additional file 2 of Integrative pigGTEx resource with GWAS reveals genetic mechanism underlying semen quality in boars

Additional file 2: Fig. S1. The histogram showing the distribution of traits measurements across all individuals in the study population. Fig. S2. The histogram of the number of ejaculation records per sire. Fig. S3. The accuracy of genotype imputation. Fig. S4. The heatmap of kinship relationships among individuals. Fig. S5. The PCA before (left) and after (right) imputation using the Pig Genotype Reference Panel (PGRP). Fig. S6. The π1 statistic for discovery in validation population or validation in discovery population. Fig. S7. The significant enrichment of GO term and KEGG pathway for individual GWAS in all semen quality traits. Fig. S8. Functional annotation and variant classification for SPPMOT, SPDCD, and SPTACOIL. Fig. S9. The most significant colocalization signal (rs341819301) of DCAF12 and top eQTL (rs318690665) of DCAF12 significantly contribute to the regulation of DCAF12 expression levels. Fig. S10. The effect of the three different genotypes of rs341819301 on the phenotypic variation of SPTACOIL, SPPMOT, and SPDCD. Fig. S11. The chromatin states of each tissue in the candidate QTL region identified in the GWAS results for SPPMOT, SPTACOIL, and SPDCD are shown. Fig. S12. The PheWAS of rs341819301 in pig. Fig. S13. The expression level of DCAF12 in multiple tissues. Fig. S14. The number of significant gene-tissue-phenotype pairs identified in each tissue for TWAS of each trait. Fig. S15. The Manhattan plot for SPMOT GWAS. Fig. S16. The conditional GWAS regional Manhattan plot for rs1112922792 in SPMOT. Fig. S17. Functional annotation and variant classification for SPMOT. Fig. S18. The gene-based association analysis for SPMOT. Fig. S19. The upsetR summary of GWAS and post-GWAS in SPMOT. Fig. S20. The eQTL mapping results for ZSCAN9 in uterus tissue. Fig. S21. The most significant colocalization signal (rs322211455) of ZSCAN9 and top eQTL (rs1112922792) of ZSCAN9 significantly contribute to the regulation of ZSCAN9 expression levels. Fig. S22. The impact of the three genotypes of rs322211455 (the colocalization signal in ZSCAN9) and rs1112922792 (the lead SNP in the SPMOT GWAS) on the phenotypic variation of SPMOT. Fig. S23. The PheWAS of rs322211455 in pig. Fig. S24. The expression level of ZSCAN9 in multiple tissues.