Comprehensive transcriptome of muscle development in Sichuan white rabbit

TL;DR

This study maps the transcriptome of muscle development in Sichuan white rabbits to understand the genetic and regulatory mechanisms behind muscle growth.

Contribution

The study provides a comprehensive transcriptomic dataset of mRNAs, miRNAs, and lncRNAs during three developmental stages in Sichuan white rabbits.

Findings

Differential expression analysis identified 2,995 DE genes, 1,211 DE-lncRNAs, and 305 DE-miRNAs across developmental stages.

Functional enrichment analysis linked DE mRNAs and miRNAs to muscle growth, development, and regeneration.

Interaction analysis revealed a complex regulatory network between DE-lncRNAs and mRNAs, especially between 21 and 27 days of development.

Abstract

The Sichuan white rabbit is a unique domestic breed and is famous for its high meat production. Muscle development is a complicated biological process, but the underlying regulatory mechanisms have not been elucidated. Here, we generated comprehensive transcriptome datasets (i.e., mRNAs, miRNAs and lncRNAs) in three developmental stages of Sichuan white rabbits, and aim to systematically explore the regulatory network in myogenesis.

We generated extensive transcriptome datasets (mRNAs, miRNAs and lncRNAs) revealing the myogenic regulatory network at different time points. Our differential expression analysis identified 2,995 DE genes, 1,211 DE-lncRNAs, and 305 DE-miRNAs with distinct expression patterns across developmental stages. In addition, functional enrichment analysis of DE mRNAs and miRNAs indicates their involvement in muscle growth, development, and regeneration, highlighting biological processes and muscle-specific functions. Interaction analysis between DE-lncRNAs and mRNAs uncovered a complex regulatory network, especially between 21 and 27 days of development. These findings contribute to better understanding of the transcriptomic changes during muscle development and have implications for breeding improvement in Sichuan white rabbits.

Our study provides a comprehensive overview of the transcriptomic changes during muscle development in Sichuan white rabbits. The identification and functional annotation of DE genes, miRNAs, and lncRNAs provide valuable insights into the molecular mechanisms underlying this process. These findings pave the way for targeted investigations into the role of non-coding RNAs in muscle biology.

The online version contains supplementary material available at 10.1186/s12863-025-01322-5.

Figures