Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs

Table 3 Description of the percentage and number of cis- and trans-eQTLs (expression quantitative trait loci) identified across scenarios represented by different set of SNPs associated with gene expression levels in the skeletal muscle of Large White pigs

eQTLs Expression quantitative trait loci, SNPs Single nucleotide polymorphisms, S2 SNPs from the RNA-seq data of the skeletal muscle, S3 SNPs from the GGP-50K plus the SNPs from the RNA-seq data of the skeletal muscle, S4 SNPs from the GGP-50K plus the SNPs from the RNA-seq data of the skeletal muscle, liver, and brain tissues; S6: SNPs from the RNA-seq data of the skeletal muscle after linkage disequilibrium (LD) pruning; S7: SNPs from the GGP-50K plus the SNPs from the RNA-seq data of the skeletal muscle after LD pruning, and, S8: SNPs from the GGP-50K plus the SNPs from the RNA-seq data of the skeletal muscle, liver, and brain tissues after LD pruning. The table diagonal represents the number of eQTLs identified, the values above the diagonal indicate the percentage of overlapping eQTLs among the scenarios, and the values below the diagonal represent the number of overlapping eQTLs across datasets

ISSN: 1471-2164