Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc × Pietrain pig resource population

To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~5.5 months of age) from a Duroc × Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1 × 50 bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74.8% of total reads mapping successfully. The miRDeep2 software package was utilized to quantify annotated Sus scrofa mature miRNAs from miRBase (Release 21) and to predict candidate novel miRNA precursors. Among the retained 295 normalized mature miRNA expression profiles ssc­miR­1, ssc­miR­133a­3p, ssc­miR­378, ssc­miR­206, and ssc­miR­10b were the most abundant, all of which have previously been shown to be expressed in pig skeletal muscle. Additionally, 27 unique candidate novel miRNA precursors were identified exhibiting homologous sequence to annotated human miRNAs. The composition of classes of small RNA present in this dataset was also characterized; while the majority of unique expressed sequence tags were not annotated in any of the queried databases, the most abundantly expressed class of small RNA in this dataset was miRNAs. This data provides a resource to evaluate miRNA regulation of gene expression and effects on complex trait phenotypes in adult pig skeletal muscle. The raw sequencing data were deposited in the Sequence Read Archive, BioProject PRJNA363073

Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs

Abstract Background Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, little is known about the genes and molecular mechanisms involved in this process. Evaluating transcriptomic profiles of skeletal muscle during the initial steps leading to the conversion of muscle to meat can identify key regulators of polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker genotypes allows identification of genomic regions that control gene expression, referred to as expression quantitative trait loci (eQTL). In this study, we perform eQTL analyses to identify potential candidate genes and molecular markers regulating growth and meat quality traits in pigs. Results Messenger RNA transcripts obtained with RNA-seq of longissimus dorsi muscle from 168 F2 animals from a Duroc x Pietrain pig resource population were used to estimate gene expression variation subject to genetic control by mapping eQTL. A total of 339 eQTL were mapped (FDR ≤ 0.01) with 191 exhibiting local-acting regulation. Joint analysis of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for meat quality, carcass composition and growth traits. Ten of these pQTL were for meat quality phenotypes that co-localized with one eQTL on SSC2 (8.8-Mb region) and 11 eQTL on SSC15 (121-Mb region). Biological processes identified for co-localized eQTL genes include calcium signaling (FERM, MRLN, PKP2 and CHRNA9), energy metabolism (SUCLG2 and PFKFB3) and redox hemostasis (NQO1 and CEP128), and results support an important role for activation of the PI3K-Akt-mTOR signaling pathway during the initial conversion of muscle to meat. Conclusion Co-localization of eQTL with pQTL identified molecular markers significantly associated with both economically important phenotypes and gene transcript abundance. This study reveals candidate genes contributing to variation in pig production traits, and provides new knowledge regarding the genetic architecture of meat quality phenotypes