Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

• Published in: PloS one Vol. 15; no. 5; p. e0233372
• Main Authors: Zappaterra, Martina, Gioiosa, Silvia, Chillemi, Giovanni, Zambonelli, Paolo, Davoli, Roberta
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19-05-2020; Public Library of Science (PLoS)
• Subjects: Adipocytes; Adipose tissue; Animal sciences; Animal species; Animal welfare; Backup software; Biology and Life Sciences; Cell differentiation; Cilia; Composition; Councils; Deposition; Differentiation (biology); Divergence; Fibroblast growth factor 2; Fibroblast growth factors; Food; Gene expression; Gene regulation; Gene sequencing; Genes; Genetic aspects; Genomes; Genomics; Growth factors; Hogs; Identification and classification; Meat; Meat products; Meat quality; Medicine and Health Sciences; Metabolism; Methods; Modules; Muscles; Myogenesis; Organelles; Overexpression; Physiological aspects; Pork; Regulatory genes; Ribonucleic acid; RNA; RNA processing; RNA sequencing; Splicing; Sus scrofa; Swine; Transcription; Transcription (Genetics); Zoology; Italy; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0233372

Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analyzing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 ± 0.09% in low IMF vs. 6.81 ± 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analyzed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and G-protein and ERK signaling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of the Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes in the significant modules confirmed the results obtained for the DEGs, and the analysis with "cytoHubba" indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation.