Comparative Analysis of miRNA Expression Profiles in Skeletal Muscle of Bian Chickens at Different Embryonic Ages
by
, , ,
Kai-Zhi Zhou
1
,
Peng-Fei Wu
1
,
Xin-Chao Zhang
1,
Xuan-Ze Ling
1,
Jin Zhang
1,
Li Zhang
2,
Pei-Feng Li
2,
Tao Zhang
1,
Qing-Yu Wei
2 and
Gen-Xi Zhang
1,* 
1
College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
2
College of Animal Science, Shanxi Agricultural University, Taiyuan 030032, China
*
Author to whom correspondence should be addressed.
Animals 2022, 12(8), 1003; https://doi.org/10.3390/ani12081003
Submission received: 16 February 2022
/
Revised: 5 April 2022
/
Accepted: 11 April 2022
/
Published: 13 April 2022
(This article belongs to the Special Issue Biotechnology and Bioinformatics in Livestock)
Simple Summary
The development of skeletal muscle during the embryonic period has an important impact on the meat production of poultry, and miRNAs are vital regulators of skeletal muscle development. In this study, through the RNA-seq analysis of leg muscles from 14- and 20-day Bian chicken embryos, we screened out 127 and 131 differentially expressed miRNAs (DEMs) in a fast-growing group (F14 vs. F20) and a slow-growing group (S14 vs. S20), respectively. Based on functional enrichment analysis and interaction network analysis, we further screened out 13 miRNAs and 5 hub genes, which potentially play important roles in skeletal muscle development. This study provides data support for future studies on the regulatory mechanisms of miRNAs in the skeletal muscle development of Bian chickens.
Abstract
MicroRNAs (miRNAs) are widely involved in the growth and development of skeletal muscle through the negative regulation of target genes. In order to screen out the differentially expressed miRNAs (DEMs) associated with skeletal muscle development of Bian chickens at different embryonic ages, we used the leg muscles of fast-growing and slow-growing Bian chickens at the 14th and 20th embryonic ages (F14, F20, S14 and S20) for RNA-seq. A total of 836 known miRNAs were identified, and 121 novel miRNAs were predicted. In the F14 vs. F20 comparison group, 127 DEMs were screened, targeting a total of 2871 genes, with 61 miRNAs significantly upregulated and 66 miRNAs significantly downregulated. In the S14 vs. S20 comparison group, 131 DEMs were screened, targeting a total of 3236 genes, with 60 miRNAs significantly upregulated and 71 miRNAs significantly downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the predicted target genes were significantly enriched in 706 GO terms and 6 KEGG pathways in the F14 vs. F20 group and 677 GO terms and 5 KEGG pathways in the S14 vs. S20 group. According to the interaction network analysis, we screened five coexpressed DEMs (gga-miR-146a-3p, gga-miR-2954, gga-miR-34a-5p, gga-miR-1625-5p and gga-miR-18b-3p) with the highest connectivity degree with predicted target genes between the two comparison groups, and five hub genes (HSPA5, PKM2, Notch1, Notch2 and RBPJ) related to muscle development were obtained as well. Subsequently, we further identified nine DEMs (gga-let-7g-3p, gga-miR-490-3p, gga-miR-6660-3p, gga-miR-12223-5p, novel-miR-327, gga-miR-18a-5p, gga-miR-18b-5p, gga-miR-34a-5p and gga-miR-1677-3p) with a targeting relationship to the hub genes, suggesting that they may play important roles in the muscle development of Bian chickens. This study reveals the miRNA differences in skeletal muscle development between 14- and 20-day embryos of Bian chickens from fast- and slow-growing groups and provides a miRNA database for further studies on the molecular mechanisms of the skeletal muscle development in Bian chickens.
Keywords:
miRNA-seq; skeletal muscle; Bian chicken; growth and development
