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

Abstract

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 "cyto-Hubba" 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.

Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile

“…A range from 92.80% to 94.50% of the reads mapped to the porcine reference genome was used ( Table S2 ). These results agree with the previous study carried out in the same tissue of pigs from the same population but in different individuals (except L7) [ 24 ] and with a study carried out in Semimembranosus muscle tissue on Large White pigs [ 32 ].…”

Investigating the Features of PDO Green Hams during Salting: Insights for New Markers and Genomic Regions in Commercial Hybrid Pigs

“…Primary cilia are non-motile organelles that have been shown to play an important role as antennae to extracellular stimuli during embryogenesis [ 53 ], adipogenesis, and myofibrogenesis [ 54 ]. In our previous study, we found several genes related to primary cilia associated with intramuscular fat deposition [ 55 ], and NEDD9 may take part in this complex signaling pathway related to muscle and adipose tissue development in embryogenesis. Interestingly, the marker ASGA0031014 fell into an intronic region harboring several sequences recognized by FOXO transcriptional regulators.…”

Muscle Transcriptome Analysis Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Pigs

“…In pigs, WGCNA was also employed to analyze a number of complex traits, such as feed efficiency ( Xu Y. et al, 2018 ; Banerjee et al, 2020 ; Carmelo et al, 2020 ), heat tolerance ( He et al, 2020 ), residual feed intake ( Liu H. et al, 2016 ), and obesity ( Kogelman et al, 2014 ). However, so far, only one study was found that have used WGCNA to analyze IMF content in Italian Large White pigs ( Zappaterra et al, 2020 ).…”