Transcriptomic gene profiling of porcine muscle tissue depending on histological properties

Abstract

In pig, the histological profile of muscle tissue, especially the proportion of individual fiber types, is one of the main factors affecting meat quality properties. In the present research, RNA sequencing (RNA-seq) by using next generation sequencing method was applied to estimate the whole gene expression profile of Longissimus lumborum muscle of pigs (Large White breed) differing in the percentage of two fiber types (slow-twitch (type I) fibers and fast-twitch glycolytic (type IIB) fibers). The RNA-seq approach allowed us to identify 355 differentially expressed genes (DEGs) indicated as significant (false discovery rate-adjusted P < 0.05) using three types of software: DESeq2, edgeR and baySeq. Detected genes and pathways deregulated in muscle depending on tissue microstructure were associated with: metabolic processes - 158 genes; cellular processes - 122; biological regulation - 62; localization - 51; and 35 genes with developmental processes. The DEGs were included in: PI3K-Akt; FoxO and MAPK signaling pathways, regulation of actin cytoskeleton, lysine degradation and insulin signaling pathway as well as mTOR and Hippo signaling pathways. These results highlight the mainly metabolic pathways related to glucose metabolism and contraction processes of muscle cells. Detection of genes involved in variation of fiber-type distribution will be useful in understanding of the genetic factors affecting muscle structure, metabolic process and indirectly, meat quality traits.

Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

“…ACTG1, ACTN2, and ACTN3, the most significant differential expression of unigenes critical for the regulation of actin cytoskeleton pathway was observed. Actin and actin-related proteins have been shown to control various cellular processes, including cell volume changes, cell size, and motility [31]. For the Msc_4 vs. Msc_3 comparison, the top gene-gene interaction network was found to be involved in the cAMP signaling pathway, the Calcium signaling pathway, and Viral carcinogenesis.…”

Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data

“…The SNPs in coding and untranslated regions (UTR) were identified based on RNA-seq data obtained previously by Ropka-Molik et al [ 13 ]. Whole transcriptome sequencing was performed on longissimus lumborum samples collected from 11 Large White pigs that differed in the histological structure of this muscle.…”

“…Immediately after slaughter, muscle samples were collected and stored at −20°C in RNAlater solution (Ambion Inc., Austin, TX, USA) for RNA-seq application and at −80°C for histological analysis. The details of the animals used, the RNA-seq experiment and histological analysis were described in a previous study focused on differential expression analysis [ 13 ].…”

“…For selected animals, in total 293 (Landrace n = 110, Large White n = 70, Duroc n = 20, Puławska pigs n = 93), longissimus muscle samples were collected immediately after slaughter and histological profile—percentage and diameter of the I, IIA, and IIB types of fibers—were estimated according to the procedure described previously by Ropka-Molik et al [ 13 ]. The animals used to histological analysis were randomly selected from population included in association study.…”

“…It has been well-established that percentage number of fiber types in muscle determines metabolic properties and water holding capacity of muscle tissue, as well as marbling, intramuscular fat (IMF) level, meat color and texture [ 10 – 12 ]. In our previous study performed on Large White pigs, we identified genes differentially expressed in muscle contingent on histological microstructure [ 13 ]. According to the differential expression and biological function, several genes were selected with possible effect on variation of fiber-type distribution.…”