Abstract

   Intramuscular fat (IMF) content plays an essential role in meat
   quality. For identifying potential candidate genes and pathways
   regulating IMF content, the IMF content and the longissimus dorsi
   transcriptomes of 28 purebred Duroc pigs were measured. As a result,
   the transcriptome analysis of four high- and four low-IMF individuals
   revealed a total of 309 differentially expressed genes (DEGs) using
   edgeR and DESeq2 (p < 0.05, |log[2](fold change)| ≥ 1). Functional
   enrichment analysis of the DEGs revealed 19 hub genes significantly
   enriched in the Gene Ontology (GO) terms and pathways (q < 0.05)
   related to lipid metabolism and fat cell differentiation. The weighted
   gene coexpression network analysis (WGCNA) of the 28 pigs identified
   the most relevant module with 43 hub genes. The combined results of
   DEGs, WGCNA, and protein–protein interactions revealed ADIPOQ, PPARG,
   LIPE, CIDEC, PLIN1, CIDEA, and FABP4 to be potential candidate genes
   affecting IMF. Furthermore, the regulation of lipolysis in adipocytes
   and the peroxisome proliferator-activated receptor (PPAR) signaling
   pathway were significantly enriched for both the DEGs and genes in the
   most relevant module. Some DEGs and pathways detected in our study play
   essential roles and are potential candidate genes and pathways that
   affect IMF content in pigs. This study provides crucial information for
   understanding the molecular mechanism of IMF content and would be
   helpful in improving pork quality.

   Keywords: pork quality, IMF content, RNA sequencing, differentially
   expressed genes, WGCNA

Introduction

   Meat quality is the main economic trait in pig production and can be
   evaluated by multiple indicators, such as intramuscular fat (IMF)
   content, pH, water holding capacity, color, and tenderness. Of these,
   IMF content is arguably the most important and is closely correlated to
   other meat quality traits, such as flavor, juiciness, and tenderness
   ([33]Klont et al., 1998). High levels of IMF content or marbling have a
   positive influence on the eating quality of pork ([34]Van Laack et al.,
   2001). However, for the past century, thinner backfat was considered as
   an important parameter in pig breeding. Although this selection led to
   higher muscularity and growth, IMF content, juiciness, and tenderness
   of the meat decreased ([35]Hernández-Sánchez et al., 2013). It is
   extremely difficult to improve IMF content by traditional breeding
   methods, even as consumers have become more discerning about meat
   quality. Therefore, it is worthwhile to understand the molecular basis
   of IMF content and carry out molecular breeding for satisfying consumer
   preferences.