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

Hongmei Hu,Xueyan Zhao,Yanping Wang,Haichao Lin,Cheng Wang,Jiying Wang

doi:10.3389/fgene.2020.00877

Hongmei Hu, Xueyan Zhao + Show 4 more

Open Access

https://doi.org/10.3389/fgene.2020.00877

Copy DOI

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, |log2(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.

Highlights

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
Study, we found that the regulation of lipolysis in adipocytes pathway was enriched in the high-IMF group compared with that in the low-IMF group
As the magenta module resulting from the WGCNA showed a strong association with IMF, we investigated the candidate genes that affected IMF content in this module

Summary

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. IMF content is arguably the most important and is closely correlated to other meat quality traits, such as flavor, juiciness, and tenderness (Klont et al, 1998). For the past century, thinner backfat was considered as an important parameter in pig breeding. This selection led to higher muscularity and growth, IMF content, juiciness, and tenderness of the meat decreased (Hernández-Sánchez et al, 2013).

Methods

Results

Conclusion