Liver Transcriptome Analysis Reveals Sex-Dependent Genes and Gene Networks Linked to Carcass Traits in Suckling Lambs

Sex is a relevant source of variation in carcass composition in suckling lambs; however, the molecular mechanisms underlying this early sexual dimorphism remain poorly understood. Given the central role of the liver in metabolic regulation and nutrient partitioning, this study characterized sex-specific hepatic transcriptional profiles and their relationship with carcass traits in Assaf suckling lambs. Liver RNA-seq data from 12 lambs (6 males and 6 females) harvested at commercial weight were analyzed using differential expression analysis ( DEA ) and weighted gene co-expression network analysis ( WGCNA ). Four carcass traits were evaluated: pelvic fat percentage ( PFP ), muscle percentage (MP), bone percentage ( BP ), and muscle-to-bone ratio ( MP/BP ). Females showed higher MP, whereas males had higher PFP, confirming early sexual dimorphism. DEA identified 211 differentially expressed genes, including 93 upregulated in males ( M-DEGs ) and 118 in females ( F-DEGs ). M-DEGs genes were enriched in cell cycle and mitotic processes, indicating a more proliferative hepatic profile. F-DEGs were enriched in pathways related to apoptosis, oxidative stress, mitochondrial targeting, and extracellular vesicle components, suggesting a stronger stress-responsive and inter-organ communication profile, possibly linked to the ongoing brown-to-white perirenal adipose tissue transition. Network analysis revealed sex-specific co-expression modules associated with carcass traits, two of which were enriched for DEGs. In males, one of these DEG-enriched modules ( green ) was negatively associated with PFP, strongly enriched for cell cycle–related functions, and included NDC80 as both a hub gene and M-DEG, supporting a possible link between hepatic proliferative activity and reduced fat deposition. In females, another DEG-enriched module ( pink ) was negatively associated with BP and positively with MP/BP, with FYN as its top hub gene, highlighting biological processes potentially involved in bone remodeling and muscle growth. Although these results should be considered hypothesis-generating, they indicate that sex-biased hepatic gene networks may be associated with early variation in carcass composition and may support a role for liver-mediated mechanisms in the establishment of postnatal carcass sexual dimorphism in suckling lambs.