MiRNA\u2013mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome

Yifan Liu,Jianmin Zou,Xiaojun Ju,Zhongwei Sheng,Yanju Shan,Jingfang Xie,Ming Zhang,Jingting Shu,Yunjie Tu,Gaige Ji

doi:10.1038/s41598-020-67482-9

Abstract

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.

Highlights

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality
We used Illumina deep sequencing to analyze the protein-coding transcript abundance in eight libraries based on the pectoralis major muscle (PMM) and SART extracted from four Qingyuan partridge hens
The GC contents of the clean data ranged from 46.7 to 49.0%, and the clean read quality scores of Q20 and Q30 were above 98.6% and 95.2%, respectively, demonstrating that the reliability and quality of the sequencing data were adequate for further analysis

Summary

Introduction

Skeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. We used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens. We compared the miRNA and mRNA differences between pectoralis major muscle (PMM) of the glycolytic type and sartorius muscle (SART) of the oxidative type and identify the key miRNA-mediated mechanism for muscle fiber type regulation. This work would contribute to the understanding of chicken meat quality control and improvement

Methods

Results

Conclusion