Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition from transcriptomic and proteomic profiles in Dingyuan pigs

Purpose: This study conducted RNA-Seq analysis on Dingyuan pig individuals with different intramuscular fat content and backfat thickness, in order to find genes that specifically regulate subcutaneous fat and intramuscular fat deposition in pigs Overall design: we used RNA Seq and TMT-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We found 191 differential genes (DEGs) in the HBF (high back fat thickness) group and LBF (low back fat thickness) group. In the HIMF (high intramuscular fat) and LIMF (low intramuscular fat) groups, we found 85 DEGs . The enrichment analysis of GO and KEGG showed that DEGs of the BF group are mainly involved in various metabolic pathways such as carbohydrates, amino acids, esters and fatty acids, while the DEGs of the IMF group are involved in a wide range of signal pathways, including metabolic pathways, the insulin and the synthesis and degradation of ketone bodies, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters and fatty acids, we have found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes specifically regulate intramuscular fat deposition in Dingyuan pigs.Our data provide insights for analyzing the mechanism of pig fat deposition