Identification of expression quantitative trait loci for longissimus muscle microrna expression profiles in the Michigan State University Duroc × Pietrain pig resource population

MicroRNAs (miRNAs) are a class of small, non-coding RNAs shown to post-transcriptionally regulate gene expression through complementary binding with target mRNAs. To date, there has been little exploration of the effects of miRNA regulation in skeletal muscle of market-age pigs. The objective of this study was to conduct an expression Quantitative Trait Loci (eQTL) analysis of miRNAs expressed in the Longissimus dorsi (LD) muscle of 174 F2 pigs from the MSU Duroc x Pietrain Resource Population to identify genomic regions containing variants associated with variation in miRNA expression (miRNA eQTL). Animals selected for this study exhibited extremes for phenotypes of loin muscle area and backfat thickness. These animals were previously genotyped with Illumina PorcineSNP60 BeadChips, and markers were filtered for removal of non-informative markers, markers with extreme allele frequencies (MAF > 0.10) and markers located on sex chromosomes. Total RNA extracted from LD tissue for each pig was sequenced on an Illumina HiSeq 2500 sequencing platform in 1x50 bp, single-end format. Raw sequence reads were trimmed for adaptor sequences, size- and quality-filtered, and PCR duplicates were removed. High-quality reads were aligned to the Sus scrofa reference genome (10.2.79), and annotated Sus scrofa miRNAs (miRBase) were quantified using miRDeep2. After filtering for low abundance across samples, 295 mature miRNA expression profiles were normalized utilizing the voom function of the Limma R package, and resulting logcounts per million were treated as response variables in a GBLUP-based genome-wide association (GWA) analysis utilizing the gwaR R package developed by our group. The GBLUP model included fixed effects of sex and selection group, random additive genetic effects with variance-covariance proportional to the genomic relationship matrix, and heterogeneous independent Gaussian residuals with variance proportional to inverse weights obtained from the voom function in Limma. Results of the GBLUP analysis indicated the average heritability of the 295 miRNAs was 0.118, whereas average heritability of the 47 miRNAs exhibiting significantly heritable expression was 0.329 (q > 0.05). Twenty-six significant miRNA eQTL peaks were identified from the GWA analysis, mapping to 11 chromosomes and associated with 18 miRNAs (q > 0.05). Seven of the 26 miRNA eQTL map to a region on SSC15 (133.9 Mb- 140.1 Mb). This is the first miRNA eQTL analysis reported in pigs, and future