Fig. 4

Multi-omics analyses of candidate functional SNPs and target genes. a The overall strategy for identification of candidate functional SNPs and their corresponding target genes: Firstly, SNPs located within loop-mediated CREs were screened. Secondly, the resultant SNPs located in ATAC peaks or footprints were further screened. Thirdly, the obtained SNPs with |ΔAF|≥0.5 (between commercial lean pig breeds and Chinese local pig breeds) were retained. Fourthly, the retained SNPs whose corresponding target genes were related to muscle traits and had intra-chromosomal RNA-chromatin interactions were screened. Fifthly, those SNPs which were predicted to affect TF binding were identified as final candidate SNPs. b Circos plot of 15 muscle-related traits, 54 target genes, and 223 candidate functional SNPs across the genome. Promoter track (orange), enhancer track (blue), ATAC peak track (green), and three categories of genes are labeled. c Example of PRKAG3 in LW and MS. Red indicates newly-identified candidate functional SNPs and target genes in this study. Orange denotes previously predicted functional SNPs and target genes identified by GWAS. The blue bar highlights the candidate functional SNPs. d Predicted SNP affecting the motif of PKNOX1. e Example of PRRX1 in LW and MS. Red indicates newly-identified functional SNPs and target genes in this study. Orange denotes previously predicted functional SNPs and target genes by GWAS. The blue bar highlights the candidate functional SNPs. f Predicted SNPs affecting the motifs of SIX2 and TEAD1