Comparative analyses of longissimus muscle miRNAomes reveal microRNAs associated with differential regulation of muscle fiber development between Tongcheng and Yorkshire pigs.

Yu Xi,Ji Li,Wenchao Li,Jiayong Lin,Jinlong Zhang,Guorong Liu,Wanghong Liu,Huijing Liu,Debin Ni,Yuqiang Zhao,Minggang Lei,Andre Van Wijnen

doi:10.1371/journal.pone.0200445

Abstract

Tongcheng (TC) and Yorkshire (YK) are two pig breeds with distinctive muscle morphology. Porcine microRNAome (miRNAome) of the longissimus muscle during five developmental stages (40, 55, 63, 70, and 90 days post coitum (dpc)) was explored by Solexa sequencing in the present study to find miRNAs involved in the different regulation of skeletal muscle development between the two breeds. A total of 320 known porcine miRNAs, 64 miRNAs corresponding to other mammals, and 224 potentially novel miRNAs were identified. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) suggested that the factor “pig breed” affected the miRNA expression profiles to a lesser extent than the factor “developmental stage”. Fifty-seven miRNAs were differentially expressed (DE) between the neighbor developmental stages in TC and 45 such miRNAs were found in YK, 34 in common; there were more down-regulated stage-DE miRNAs than up-regulated. And a total of 23, 30, 12, 6, and 30 breed-DE miRNAs between TC and YK were identified at 40, 55, 63, 70, and 90 dpc, respectively, which were mainly involved in cellular protein modification process, protein transport, and metabolic process. As the only highly expressed breed-DE miRNA found in no less than four developmental stages, and also a stage-DE miRNA found both in TC and YK, miR-499-5p could bind the 3’-UTR of a myofibrillogenesis regulator, destrin/actin depolymerizing factor (DSTN), as validated in dual luciferase reporter assay. The results suggested that miR-499-5p possibly play a noteworthy role in the breed-distinctive porcine muscle fiber development associated with the regulation of DSTN.

Highlights

Muscle development in various types of pig breeds is associated with specific differences in the quality of the meat, such as the taste
Breed-specific differentially expressed (DE) miRNAs found at any of the five developmental stages were respectively paired with their software-predicted gene/mRNA targets (Figure A in S1 Fig), based on the negative correlation (Spearman’s correlation coefficient
The results showed that as the only highly expressed breed-DE miRNA found in no less than four developmental stages, and a stage-DE miRNA found both in TC and YK, miR-499-5p exhibited direct affinity for binding to the 3’-UTR of DSTN, suggesting that miR-499-5p possibly play a noteworthy role in the breed-distinctive porcine muscle fiber development associated with the regulation of DSTN

Summary

Introduction

Muscle development in various types of pig breeds is associated with specific differences in the quality of the meat, such as the taste. Yorkshire (YK), an exotic purebred pig breed, has fast-growing muscles that lead to high lean meat percentage and relatively lower meat quality [2]. Analyses of the development differences in skeletal muscles between them may help the identification of the cellular mechanisms underlying meat quality. These analyses may be beneficial for the improvement of pork production. Molecular mechanisms regulating the formation and transition of muscle fibers with time may greatly contribute to meat quality and muscle growth rate

Objectives

Results

Discussion

Conclusion