Transcriptome analysis reveals key genes and regulatory networks underlying intramuscular fat deposition in rabbits

Intramuscular fat (IMF) is a critical determinant of meat quality in rabbits, influencing attributes such as tenderness, juiciness, and flavor. A moderate increase in IMF content is associated with enhanced meat quality. In this study, we evaluated the growth performance, slaughter performance, and meat quality traits of the longissimus dorsi (LD) muscles in Hycole and Rex rabbits across various growth stages. Utilizing transcriptome sequencing, we identified and analyzed differentially expressed mRNAs (DE mRNAs) and long non-coding RNAs (DE lncRNAs), and constructed lncRNA-mRNA regulatory networks to investigate candidate genes influencing IMF content in Rex rabbits at different developmental stages. The results demonstrated an age-dependent increase in IMF content for both breeds, with Rex rabbits consistently exhibiting higher IMF levels compared to Hycole rabbits at equivalent ages. Through whole transcriptome sequencing, we identified several DE mRNAs and DE lncRNAs associated with fat deposition across various developmental stages and breeds. These include KCNQ5, POSTN, TMEM182, CASQ2, ME1, and COL6A6, as well as lncRNAs such as TCONS₀0009631, TCONS₀0082976, TCONS₀0040377, TCONS₀0051990, and TCONS₀0069025. Enrichment analysis revealed that these genes are implicated in key signaling pathways related to fat deposition, including the Wnt, TGF-β, and PPAR signaling pathways. RNA sequencing data further revealed that age significantly impacts IMF deposition, with the most pronounced differences observed between 35-day-old and 150-day-old rabbits. Additionally, through comprehensive lncRNA-mRNA regulatory network, short time-series expression miner (STEM) analyses, and weighted gene co-expression network analysis (WGCNA), we identified 10 lncRNA-mRNA target gene pairs associated with IMF deposition, including critical genes implicated in fat accumulation such as STARD13, HSPB8, and CBLB. This work provided regulatory networks of rabbits and revealed STARD13, HSPB8, and CBLB as the key genes responsible for IMF deposition. Our findings highlight that IMF deposition in rabbits triggers dynamic transcriptional alterations. These findings provide a robust theoretical foundation for advancing genetic breeding strategies and elucidating the regulatory mechanism underlying adipose development in rabbits.