Transcriptome analysis of long non-coding RNA associated with embryonic muscle development in chickens

ABSTRACT

1. Skeletal muscle is an important component of chicken carcass. In chickens, the number of muscle fibres is fixed during the embryonic period, and muscle development during the embryonic period determines the muscle development potential after hatching.

2. Beijing-You (BY) and Cornish (CN) chickens show completely different growth rates and body types, and two breeds were used in this study to explore the role of lncRNAs in muscle development during different chicken embryonic periods. A systematic analysis of lncRNAs and mRNAs were conducted in the pectoral muscle tissues of BY and CN chickens at embryonic days 11 (ED11), 13 (ED13), 15 (ED15), 17 (ED17), and 1-day-old (D1) using RNA-seq. A total of 4,104 differentially expressed transcripts (DETs) were identified among the five stages, including 2,359 lncRNAs and 1,745 mRNAs.

3. The number of DETs between the two breeds at ED17 (1,658 lncRNAs and 1,016 mRNAs) was much higher than the total number of DET at all the other stages (692 lncRNAs and 729 mRNAs), indicating that the two breeds show the largest difference in gene regulation at ED17.

4. Correlation analysis was performed for all differentially expressed lncRNAs and mRNAs during the five periods. Forty-three, cis interaction pairs of lncRNA-mRNA related to chicken muscle development were predicted. The expression of four pairs was verified, and the results showed MSTRG.12395.2-FGFBP2 and MSTRG.18590.6-FMOD were significantly up-regulated in CN at ED11 compared to BY and might be important candidate genes for embryonic muscle development.

KEYWORDS:

• Chicken
• embryonic
• muscle fibre
• lncRNA
• target gene

Abbreviations

lncRNAs: Long non-coding RNAs; CN: Cornish chicken; BY: Beijing You chicken; ED11: embryonic days 11; ED13: embryonic days 13; ED15: embryonic days 15; ED17: embryonic days 17; D1: 1-day-old; GTF: General Transfer Format; PCA: Principal component analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; DElncRNAs: differentially expressed lncRNAs; DEGs: differentially expressed genes; DET: differentially expressed transcripts.

Disclosure statement

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

Data availability statement

All the RNA-seq sequencing data have been deposited in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under accession numbers PRJNA1011384.

Author contributions

YMY analysed the data and drafted the original manuscript. WQD performed the research. CJS, QHN and JL provided comments on the experiment. LL and NY designed the experiment and revised the original manuscript. All authors provided revisions in finalising the manuscript.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/00071668.2024.2335935

Additional information

Funding

This work was financially supported by National Natural Science Foundation of China [U1901206, 32272865], the National Key Research and Development Program of China [2022YFF1000200 and 2021YFD1300600], Agriculture Research Systems [CARS-40], Farm Animals Germplasm Resource Platform, the Programs for Chang jiang Scholars and Innovative Research Team in University [IRT_15R62].