Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Jie Li; Chuwen Chen; Ruipeng Zhao; Jinbo Wu; Zhixiong Li

doi:10.3389/fphys.2023.1225349

Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages

Front Physiol. 2023 Jul 26:14:1225349. doi: 10.3389/fphys.2023.1225349. eCollection 2023.

Authors

Jie Li^{1

2}, Chuwen Chen^{1

2}, Ruipeng Zhao^{1

3}, Jinbo Wu⁴, Zhixiong Li^{1

2}

Affiliations

¹ Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, Sichuan, China.
² College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China.
³ Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China.
⁴ Institute of Science and Technology of Aba Tibetan and Qiang Autonomous Prefecture, Aba Sichuan, China.

Abstract

Introduction: As a valuable genetic resource, native birds can contribute to the sustainable development of animal production. Tibetan chickens, known for their special flavor, are one of the important local poultry breeds in the Qinghai-Tibet Plateau. However, Tibetan chickens have a slow growth rate and poor carcass traits compared with broilers. Although most of the research on Tibetan chickens focused on their hypoxic adaptation, there were fewer studies related to skeletal muscle development. Methods: Here, we performed the transcriptional sequencing of leg muscles from Tibetan chicken embryos at E (embryonic)10, E14, and E18. Results: In total, 1,600, 4,610, and 2,166 DE (differentially expressed) mRNAs, 210, 573, and 234 DE lncRNAs (long non-coding RNAs), and 52, 137, and 33 DE miRNAs (microRNAs) were detected between E10 and E14, E10 and E18, and E14 and E18, respectively. Functional prediction showed several DE mRNAs and the target mRNAs of DE lncRNAs and DE miRNAs were significantly enriched in sarcomere organization, actin cytoskeleton organization, myofibril, muscle fiber development, and other terms and pathways related to muscle growth and development. Finally, a lncRNA-miRNA-mRNA ceRNA (competing endogenous RNA) network associated with muscle growth and development, which contained 6 DE lncRNAs, 13 DE miRNAs, and 50 DE mRNAs, was constructed based on the screened DE RNAs by Gene Ontology (GO) enrichment. These DE RNAs may play a critical regulatory role in the skeletal muscle development of chickens. Discussion: The results provide a genomic resource for mRNAs, lncRNAs, and miRNAs potentially involved in the skeletal muscle development of chickens, which lay the foundation for further studies of the molecular mechanisms underlying skeletal muscle growth and development in Tibetan chickens.

Keywords: ceRNA; chicken; lncRNA; mRNA; miRNA; skeletal muscle growth and development.

Grants and funding

This research was funded by the Natural Science Foundation of Sichuan Province (2023NSFSC1142), the Science and Technology Support Program of Sichuan Province (2021YFYZ0031 and 2023YFSY0048), and the Southwest Minzu University Double World-Class Project (XM2023011).