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

Abstract

Abstract Background Mapping expression quantitative trait loci (eQTL) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variations and phenotypic expression of carcass traits. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including those pruned for linkage disequilibrium (LD), derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues on the identification of eQTL in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. SNPs identified from muscle mRNA were combined with SNPs identified in brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50K array. Cis- and trans-eQTL were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. Results The number of cis- and trans-eQTL identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTL in at least one of the scenarios evaluated. The eQTL identified were not significantly associated with carcass and body composition traits based on the association analyses but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios, identified in the mRNA of muscle. These genes include 84 transcription factor coding genes. Conclusions After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTL. Most eQTL are of the trans type and are involved in genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTL that were not identified based on the porcine skeletal muscle transcriptome alone.