miRNA-mRNA associations with inosine monophosphate specific deposition in the muscle of Jingyuan chicken

ABSTRACT

1. Inosine monophosphate (IMP), is an essential component for meat flavour and microRNAs (miRNAs) play a vital role in its post-transcriptional regulation. However, the mechanism of how miRNA expression affects muscle-specific IMP deposition is unclear.

2. The following study performed transcriptome sequencing and bioinformatics analysis of breast and leg muscle, which have significantly different IMP content in Jingyuan chicken. The differential miRNA-mRNAs were screened out and correlation analysis with IMP content was performed.

3. A total of 39 differentially expressed miRNAs (DE miRNAs) and 666 differentially expressed mRNAs (DE mRNAs) were identified between breast muscles and leg muscles. Using miRNA-mRNA integrated analysis, 29 miRNA-target gene pairs were obtained, composed of 13 DE miRNAs and 28 DE mRNAs. Next, purine metabolism, glycolysis/gluconeogenesis, pyruvate metabolism and the biosynthesis of amino acid pathways as necessary for muscle IMP-specific deposition were identified. The differentially expressed gene PKM2, which was significantly enriched in all four pathways, is involved in IMP anabolism in the form of energy metabolism and enzyme activity regulation. The correlation analysis suggested that the gga-miR-107-3p-KLHDC2 negative interaction may be a key regulator in IMP deposition.

4. This study explores the functional mechanism of IMP-specific deposition in Jingyuan chicken muscles at the miRNA and mRNA levels and highlights multiple candidate miRNAs and mRNAs for molecular-assisted breeding.

KEYWORDS:

• Jingyuan chicken
• miRNA
• mRNA
• inosine monophosphate (IMP)
• miRNA-mRNA association analysis

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All data generated or analysed in this study were included in this article, and the datasets have been submitted to the NCBI database with the accession number PRJNA788204. Access to the data of permanent link to https://www.ncbi.nlm.nih.gov/bioproject/PRJNA788204.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/00071668.2022.2106777

Additional information

Funding

This study was supported by the National Nature Science Foundation of China (Grant No. 31860621) and by the Ningxia Poultry and Egg Industry Chief Expert Team Project.