Transcriptomic Analysis in the Liver of Two Rabbit Lines Divergently Selected for Intramuscular Fat Content

The intramuscular fat (IMF) content is an important indicator of meat quality, affecting the sensory properties of meat. IMF is a complex trait with polygenic nature. This research aimed to identify differentially expressed (DE) genes and key transcription factors (TFs) associated with IMF deposition in the liver of two rabbit lines divergently selected for IMF (high-IMF: H and low-IMF: L). We used 48 rabbits (24 H and 24 L) belonging to the 9th generation of selection to determine their liver gene expression levels using 3' RNA sequencing. We found 263 DE genes between H and L lines; 114 upregulated and 149 downregulated in the H line. Among them, over 30 genes were related to lipid metabolism, energy homeostasis, glutathione-purine metabolism, and/or molecule transport that could influence the IMF deposition. Of the 263 DE genes, 175 target genes were predicted for 11 DE TFs through the gene regulatory networks. Notably, three TFs, namely ETV1, NR4A1, and IKZF3 appear to modulate gene expression of several putative targets involved in lipid and energy metabolism (e.g., CREM, GDF15, and NR4A2). Functional analysis of DE genes revealed an overrepresentation of 37 enriched terms, including the PPAR signalling pathway (associated genes: CPT1B, CYP4A6, FABP4, and PLIN2) and other lipid metabolism bioprocesses. Collectively, our results enhance the understanding of the liver-muscle crosstalk that contributes to IMF deposition and improvement of rabbit meat quality.