Identification of Key Genes Related to Intramuscular Fat Content of Psoas Major Muscle in Saba Pigs by Integrating Bioinformatics and Machine Learning Based on Transcriptome Data

The psoas major muscle (PMM) is a piece of pork with good tenderness and high value. Intramuscular fat (IMF) content, serving as a pivotal indicator of pork quality, varies greatly among pigs within the same breed. However, there is a paucity of studies focusing on investigating the molecular mechanism of PMM IMF deposition in the same pig breed. The present study aimed to identify the potential genes related to the IMF content of PMM in low- and high-IMF Saba pigs based on transcriptome data analysis. The data used in this study were the RNA sequences of PMM from 12 Saba pigs (PRJNA1223630, from our laboratory) and gene expression profiles (GSE207279) acquired from the NCBI Sequence Read Archive database and the GEO database, respectively, together with data on the fatty acid and amino acid composition of the 12 Saba pigs' PMM. It was found that the high-IMF pigs exhibited significantly elevated levels of saturated fatty acids and (mono)unsaturated fatty acids, especially C14:0, C16:0, C20:0, C16:1, C18:1n9c, and C20:2, compared with those in the low-IMF pigs (<i>p</i> < 0.05 or <i>p</i> < 0.01). A total of 370 differentially expressed genes (DEGs) (221 up- and 149 down-regulated) were identified based on PRJNA1223630. Then, 20 hub genes were identified through protein-protein interaction (PPI) network analysis. Four potential fat-deposition-related genes (<i>DGAT2</i>, <i>PCK1</i>, <i>MELK</i>, and <i>FASN</i>) were further screened via the intersection of the candidate genes identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm and the top five genes ranked by the Random Forest (RF) method based on the 20 hub genes and were validated in the test gene set (GSE207279). The constructed mRNA (gene)-miRNA-lncRNA network, involving miRNAs (miR-103a-3p, miR-107, and miR-485-5p), lncRNAs (XIST, NEAT1, and KCNQ1OT1), and <i>FASN</i>, might be crucial for IMF deposition in pigs. These findings might delineate valuable regulatory molecular mechanisms coordinating IMF deposition and could serve as a beneficial foundation for the genetic improvement of pork quality.