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.
Keywords: Causal variant; Muscle; Pig; Regulatory mechanism; eQTL; miRNA.
Copyright © 2023 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.