Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous tissues and phenotypes, including those important to the pig industry. However, further research is needed to characterize the miRNAs expressed in pig skeletal muscle and assess their impact on the regulation of growth, carcass composition, and meat quality traits. Additionally, little is known about the genetic architecture controlling miRNA expression in pigs, which can be elucidated by combining high-density genotypic data with miRNA expression profiles from the same animals in the mapping of miRNA expression quantitative trait loci (miR-eQTL). This analysis reveals associations between genomic regions harboring single nucleotide polymorphisms (SNPs) and variation in the expression of miRNAs. By integrating mRNA expression profiles and phenotypic data from the same individuals, putative regulatory relationships can be revealed underlying variation in phenotypes relevant to pig production. In this study, our objectives were to profile and characterize the small RNA population present in longissimus dorsi (LD) skeletal muscle samples from a F2 Duroc x Pietrain resource population, and to conduct an integrated miR-eQTL analysis to identify regulators of miRNA expression and candidate genes regulating phenotypic traits in adult pig skeletal muscle.MicroRNA expression profiling was performed on total RNA extracted from (LD) muscle samples from 174 F2 pigs. The composition of small RNA classes present in this dataset was characterized through a series of homology searches against human, mouse, and pig databases. MicroRNA quantification and novel miRNA prediction was conducted, profiling the abundance of 295 known mature pig miRNAs and producing 27 unique candidate novel miRNA precursors. The 295 miRNA expression profiles were subsequently used as response variables in a GBLUP-based GWA analysis. Results for associating these miRNAs with 36,292 SNPs identified 315 significant miRNA-SNP associations (FDR < 0.05), comprising 23 significant eQTL peaks associated with 17 unique miRNAs. Five of the 23 miR-eQTL peaks were defined as local-acting, meaning the genomic positions of the significantly associated SNPs comprising the miR-eQTL peak overlapped that of the miRNA precursor transcript. We then investigated the potential effects of these miRNAs through miRNA target prediction, correlation, and colocalization analyses. Notably, one miR-eQTL miRNA exhibiting a strong local¬-acting miR-eQTL, miR-874, had predicted target genes colocalizing with previously identified phenotypic QTL for 12 production traits including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of this study revealed putative pig-novel miRNAs for further study and validation, contributing to our understanding of the miRNA landscape present in adult pig skeletal muscle. Additionally, we identified genomic regions underlying variation in miRNA expression, and candidate miRNAs and genes for future investigation of their regulatory effects on growth, carcass composition, and meat quality traits of importance to the global pig industry.
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