Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds.

Xinhua Hou,Lixian Wang,Lijun Shi,Hua Yan,Longchao Zhang,Xin Liu,Fuping Zhao,Ligang Wang,Hongmei Gao

doi:10.3390/ani11113169

Abstract

Simple SummaryVariation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding.RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.

Highlights

Pigs are a major source of meat production for human consumption
To increase meat yields and reduce costs, lean pig breeds are under intensive selection and exhibit a fast growth rate, improved feed efficiency, and more lean meat content compared to obese pig breeds
Numerous studies suggest that skeletal muscle characteristics, such as myofiber diameter, myofiber density, and intramuscular fat content (IMF), are different between lean and obese pig breeds [1,2,3,4,5,6]

Summary

Introduction

Pigs are a major source of meat production for human consumption. To increase meat yields and reduce costs, lean pig breeds are under intensive selection and exhibit a fast growth rate, improved feed efficiency, and more lean meat content compared to obese pig breeds.long-term selection leads to deterioration in the meat quality of lean pig breeds.Numerous studies suggest that skeletal muscle characteristics, such as myofiber diameter, myofiber density, and intramuscular fat content (IMF), are different between lean and obese pig breeds [1,2,3,4,5,6]. To increase meat yields and reduce costs, lean pig breeds are under intensive selection and exhibit a fast growth rate, improved feed efficiency, and more lean meat content compared to obese pig breeds. Long-term selection leads to deterioration in the meat quality of lean pig breeds. Numerous studies suggest that skeletal muscle characteristics, such as myofiber diameter, myofiber density, and intramuscular fat content (IMF), are different between lean and obese pig breeds [1,2,3,4,5,6]. Plus size, number, area, and density of muscle fibers reflect skeletal muscle development and determine meat quality [7]. Meat quality can be improved by increasing the IMF content based on intramuscular adipogenesis [2]

Methods

Discussion

Conclusion