Transcriptome analysis identifies key miRNAs involved in the regulation of rabbit intramuscular fat deposition

Intramuscular fat (IMF) is a critical determinant of rabbit meat quality, influencing tenderness, juiciness, and flavor. miRNAs are crucial for IMF synthesis by regulating genes involved in lipid deposition, but the mechanisms by which miRNAs regulate IMF deposition in rabbits remain poorly understood. This study aimed to investigate the role of microRNAs (miRNAs) in IMF deposition in Hycole rabbits (HR) and Rex rabbits (RR) at three developmental stages (35, 75, and 150 days of age) using small RNA sequencing. A total of 195 differentially expressed (DE) miRNAs were identified in HR across the three stages, including 49 co-expressed DE miRNAs (e.g., ocu-miR-29c-5p, ocu-miR-382-3p, ocu-miR-29b-3p). In RR, 222 DE miRNAs were detected, with 45 co-expressed DE miRNAs (e.g., ocu-miR-182-5p, ocu-miR-486-5p, ocu-miR-370-5p). Comparative analysis between breeds identified 128 DE miRNAs, but none were co-expressed. GO and KEGG enrichment analyses showed DE miRNAs and their target genes were significantly enriched in pathways like PI3K-Akt, MAPK, Hippo, and HIF-1, which were closely associated with lipogenesis, metabolism, and obesity. This study elucidates the transcriptional regulatory mechanisms of IMF deposition in rabbits and identifies key miRNAs influencing IMF accumulation. Our findings provide new insights into the molecular mechanisms underlying rabbit IMF deposition and offer important resources to support future genetic improvement and management strategies in rabbit production.