title: Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing.
abstract: Intramuscular fat (IMF) content in pork is an important element of consumer preference and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate differentially expressed genes (DEGs) closely related to IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements, and significant differences between extremely high (H, n = 3) and low (L, n = 3) IMF content groups were found (P < 0.0001). From multi-dimensional scaling analyses, it was observed that the relationships between H and L groups were similar to each other. Here, we identified a total of 134 genes that were differentially expressed between the groups (false discovery rate <0.05; fold change ≥2). Functional analyses with DEGs revealed that lipid metabolism (SCD and FASN) was one of the significant biological processes related to IMF content determination. In addition, we found that DEGs related to muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1 and COL15A1) were changed among individuals with extreme IMF contents. These results will aid in understanding the regulation of IMF content in pigs.
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.|College of Life Science and Biotechnology, Korea University, Seoul, 136-713, Korea.
authors.forename: K S
authors.initials: KS
authors.lastname: Lim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: K T
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: J E
authors.initials: JE
authors.lastname: Park
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: W H
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: G W
authors.initials: GW
authors.lastname: Jang
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: B H
authors.initials: BH
authors.lastname: Choi
authors.affiliation: College of Life Science and Biotechnology, Korea University, Seoul, 136-713, Korea.
authors.forename: K C
authors.initials: KC
authors.lastname: Hong
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 565-851, Korea.
authors.forename: T H
authors.initials: TH
authors.lastname: Kim
mesh_terms: D000818:Animals; D005223:Fats / Q000032:analysis*; D059014:High-Throughput Nucleotide Sequencing; D008460:Meat; D018482:Muscle, Skeletal / Q000737:chemistry*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D034421:Sus scrofa / Q000235:genetics* / Q000502:physiology; D059467:Transcriptome
chemical_list: D005223:Fats
keywords: Gene Ontology; IMF; differential expression; swine; transcriptome