Transcriptomic profiling of backfat and muscle in Lijiang pigs with divergent body size across growth stages

Backfat thickness is an important economic trait that affects pork quality and flavor. The Lijiang pig (LJP), a local breed in Yunnan province, China, exhibits variations in growth and body composition. However, the molecular basis for these variations is unclear. This study aimed to analyze transcriptome profiles of backfat at different growth stages in LJP with discrepant body size: two months (M2), four months, and six months. Firstly, we analyzed the gene expression differences and discovered a significantly highest number of differentially expressed genes (DEGs) at the M2 stage. Secondly, we identified four gene profiles with reverse expression trends in LJP populations with different body sizes, and the related genes mainly associated with immune response functionality. Thirdly, we observed a lower correlation in LJP with large body size at the M2 stage, with a specific enrichment of DEGs with high genetic differentiation related to neural activity. Finally, we correlated transcriptome profiles of muscle and backfat and discovered the lowest correlation at the M2 stage. Highly correlated genes exhibited more significant differences and were prominently enriched for immune response processes. This study unveils candidate genes linked to backfat growth in LJP, emphasizing the specificity of the early growth stage of backfat.