title: 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.
authors.affiliation: Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Katarzyna
authors.identifier: http://orcid.org/0000-0002-8555-0495
authors.initials: K
authors.lastname: Ropka-Molik
authors.affiliation: Department of Animal Genetics and Breeding, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Bereta
authors.affiliation: Department of Animal Genetics and Breeding, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Kacper
authors.initials: K
authors.lastname: Żukowski
authors.affiliation: Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Piórkowska
authors.affiliation: Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Artur
authors.initials: A
authors.lastname: Gurgul
authors.affiliation: Department of Animal Genetics and Breeding, National Research Institute of Animal Production, Balice, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Żak
mesh_terms: D000199:Actins / Q000378:metabolism; D000818:Animals; D063427:Food Quality; D015870:Gene Expression; D020869:Gene Expression Profiling; D005947:Glucose / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D020935:MAP Kinase Signaling System / Q000235:genetics; D008460:Meat; D018656:Muscle Fibers, Fast-Twitch; D018657:Muscle Fibers, Slow-Twitch; D018482:Muscle, Skeletal / Q000033:anatomy & histology; D058539:Phosphatidylinositol 3-Kinase / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D013552:Swine / Q000235:genetics* / Q000378:metabolism*; D058570:TOR Serine-Threonine Kinases / Q000235:genetics
chemical_list: D000199:Actins; D058539:Phosphatidylinositol 3-Kinase; D058570:TOR Serine-Threonine Kinases; D005947:Glucose; D008239:Lysine
keywords: Longissimus lumborum; RNA-seq; fast-twitch (type II) fibers; pig; slow-twitch (type I) fibers