Pleiotropic effects of the milk somatic cell transcriptome associated with feed efficiency and immunity in Holstein...

In the livestock industry, feed is the largest expense, driving interest in breeding more feed-efficient animals. Residual feed intake (RFI) is a widely used measure of feed efficiency, accounting for actual feed intake versus expected requirements for maintenance and production. Because feed efficiency is highly polygenic, associated genes may have pleiotropic effects on traits such as immunity, complicating breeding strategies. One way to study pleiotropy is through -omics technologies, including transcriptomics, which uses RNA sequencing (RNA-Seq) to analyze the transcriptome at specific tissue levels and time points. This study used RNA-Seq to identify differentially expressed genes (DEG) between low-RFI (n = 22) and high-RFI (n = 17) Holstein cows. A total of 36 genes were differentially expressed between groups, enriched in 28 significant metabolic pathways, most of which were immune-related, including the RIG-I-like receptor signaling pathway. We also performed QTL annotation and enrichment analyses for the DEG. Within these gene regions, 646 previously annotated QTL were identified, of which 26.7% were related to milk traits. Notably, 10 QTL were associated with feed efficiency, whereas 4 were linked to host immunity. The QTL enrichment further revealed 387 significantly enriched QTL, with the majority of the top associations related to health. In summary, this research identified candidate genes and QTL regions suggesting potential pleiotropic relationships between feed efficiency and immunity in Holstein dairy cows. These findings highlight the need for further investigation to balance productivity and health in genetic improvement programs.