An atlas of expression quantitative trait loci of microRNAs in longissimus muscle of eight-way crossbred pigs

Abstract

MicroRNAs (miRNAs) are key regulators of myocyte development and traits, yet insight into the genetic basis of variation in miRNA expression is still limited. Here, we present a systematic analysis of expression quantitative trait loci (eQTL) for miRNA profiling in longissimus muscle of pigs from an eight-breed crossed heterogeneous population. By integrating the whole-genome sequencing and miRNAomics data, we map 54 cis- and 292 trans-eQTLs at high resolution that are associated with the expression of 54 and 92 miRNAs, respectively. Twenty-three trans-acting loci are identified to affect the expression of nine myomiRs (known muscle-specific miRNAs). MiRNAs in mammalian conserved miRNA clusters are found to be subjected to regulation by shared cis-eQTLs, while the expression of mature miRNA-5p/-3p counterparts is more likely to be regulated by different cis-eQTLs. Fine mapping and bioinformatics analyses pinpoint the peak cis-eSNP of miR-4331-5p, rs344650810, which is located in its seed region, as a causal variant for the changes in expression and function of this miRNA. Additionally, rs344650810 is significantly (P < 0.01) correlated with the density and percentage of type I muscle fibers. Altogether, this study provides a comprehensive atlas of miRNA-eQTLs in porcine skeletal muscle and new insights into regulatory mechanisms of miRNA expression.