GSE107207
Whole transcriptome and miRNAome analysis of porcine muscle tissue in the terms of muscle growth and development
Purpose: The aim of present research was to identify genes potentially related with muscle growth in pig Methods: RNA-seq analysis was performed on longissimus lumborum samples collected from 13 pigs representing two sire-line breeds – Pietrain and Hampshire.  Base on dissection data, pigs were selected from a larger population in terms of weight of loin muscle to obtain the most extreme groups in each breed The cDNA libraries were constructed form 300 ng of total RNA with the use TruSeq RNA Sample Prep Kit v2 kit (Illumina) according to the protocol. The quantification of obtained libraries was performed on Qubit 2.0 (Invitrogen, Life Technologies) and TapeStation 2200 (D1000 ScreenTape; Agilent). The RNA-seq was performed in 101 single-end cycles on HiScanSQ platform (Illumina) with the use of ruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina).  Each library was sequences in 4 technical replications. The DEGs were detected using DESEq2 software and validation was performed by qPCR. Results: RNA-seq approach allowed to identify 627 and 416 DEGs between pig groups with different loin weight (pvalue <0.05; fold change=1.5) for Pietrain and Hampshire; respectively. Next, the comparison of obtained genes sets showed 43 genes identified in both breeds. The Gene Ontology analysis (Panther software) confirmed that detected genes were involved in regulation of metabolic process (18 genes), developmental growth or skeletal system development (PCOLCE; BBS2; TBX2; RBBP6; ATAF5). According to David software these genes belong to PI3K-Akt signaling, Focal adhesion and ECM-receptor interaction pathways. Conclusions: Obtained results allow to propose the panel of genes, which can be related with porcine muscle growth and development. Such analysis can be the basis of future research in terms of identification of candidate genes related with important production traits in pigs. Overall design: The muscle (longissimus dorsi) transcriptome sequencing was performed for 13 samples collected form pigs representing two breeds - Pietrain and Hampshare, using Illumina HiScan SQ in 101 single-end cycles and in 4 technical repetitions repetitions.