Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition.

Xuan Tao,Jianjun Gong,Yuekui Yang,Yan Liang,Yunfeng Lei,Kai Zeng,Xiaohui Chen,Zhijun Zhong,Xuemei Yang,Yiren Gu,Xuebin Lv,Runming Kang,Sancheng Ying,Jianhui Pang,Ramona Natacha Pena I Subirà

doi:10.1371/journal.pone.0184120

Abstract

Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.

Highlights

We found that YY has lower meat quality traits, such as PH1 (45 min postmortem), intramuscular fat (IMF), and marbling (MBL), which explains why YY’s meat is not sought after by consumers
We found that the modules significantly correlated with the phenotypic traits were enriched for the DEGs between Chinese breeds and YY, and the modules that positively correlated with the traits with higher values in YY were only enriched for the DEGs upregulated in YY itself, the same for the modules that positively correlated with the traits with higher value in Chinese breeds
Comparative statistical analysis revealed that Chinese breeds have distinct traits regarding growth performance, carcass quality, and meat quality, and they were clearly differentiated from YY by PC1 in the Principal component analysis (PCA)

Summary

Introduction

Pig meat is an important source of protein for humans. Liver, and skeletal muscles are the most important tissues and organs associated with whole-body lipid metabolism [3,4], which determine the IMF content and fatty acid (FA) profile in muscle. 001, SCCXTD-005) to X.B.L., the National Swine Industry Technology System Program (CARS-36) to X.B.L., the Special Finance of Sichuan (SASA2014CZYX001) to X.B.L., the Key Projects in the National Science & Technology Pillar Program (2015BAD03B02-10) to X.B.L and the National Natural Science Foundation of China (31301942), the Open Fund of Sichuan Provincial Key Laboratory of Animal Breeding and Genetics (SASA2015A01, 2016YSKY0138) to Y.R.G

Methods

Results

Conclusion