Phenotypic and expression QTL integration allows the refinement of loci associated with pig carcass and meat quality traits
Abstract Background: Many quantitative trait loci (QTLs) affecting pig meat and carcass quality traits have been reported. However, in most cases, the length of these phenotypic QTLs (pQTLs) is large. Hence, the identification of candidate genes and causative polymorphisms hidden behind those pQTLs remains a difficult task. Combining gene expression, phenotype and genotype data in an integrative genomics approach may help to identify regulatory networks and pathways underlying such complex traits. In the present study, we used genome-wide association study (GWAS) and linkage disequilibrium linkage analysis (LDLA) approaches to identify longissimus muscle (LM) and semimembranosus muscle (SM) expression QTLs (eQTLs). The locations of these eQTLs were compared to those of pQTLs previously mapped in the same population of commercial-type pigs. Colocalized eQTLs/pQTLs could help to identify candidate genes and pathways involved in pig carcass and meat quality trait determination. Results: Both approaches led us to identify 1,253 and 1,109 genome-wide significant eQTLs for LM and SM, respectively. We identified only one common eQTL between the two muscles and a few significant common eQTLs between methodologies : 16 in SM and 1 in LM. A total of 192 overlapping locations were identified between eQTLs and pQTLs. Colocalization highlighted some genes involved in muscle development, adipogenic processes or ion calcium homeostasis. These eQTLs allowed us to refine previously identified pQTLs related to carcass and meat quality traits. However, in most cases, the refined loci were still large and contained several coding and noncoding genes. Conclusions: Our results shed light on the muscle-specific genetic control governing mRNA expression and hence controlling the development of pig carcass and meat quality traits. Moreover, colocations between eQTLs and pQTLs implicated genes potentially involved in muscle development, adipogenic processes or ion calcium homeostasis in the pathways governing these traits. Finally, our results allowed us to refine QTLs controlling meat quality traits and to highlight the possible involvement of long noncoding RNAs in the architecture of regulatory networks governing complex traits such as pig carcass and meat quality traits.