Metabolomics Integrated with Transcriptomics Reveals a Subtle Liver Metabolic Risk in Dairy Cows Fed Different Crop By-products.

Ruminants make large contributions to sustainable agriculture by converting crop by-products into agricultural food. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. The liver metabolome-transcriptome interface (LMTI) in dairy cows, including 3938 significant correlations (p < 0.01 and |ρ| > 0.6) among 772 genes, 306 metabolites, and 305 microRNAs, is first demonstrated. How different crop by-products, corn stover (CS) and rice straw (RS), affect the liver metabolic functions based on the LMTI is further analyzed. Compared to the CS-fed cows, 13 out of 24 metabolites have lower relative concentrations (variable importance projection > 1.0 and p < 0.05), and 51 out of 68 genes are downregulated in the RS group (p < 0.01 and fold change < -2). Integrated analysis of metabolomics and transcriptomics reveal that lipid metabolism is most enriched including 14 subpathways. The altered metabolites and genes revealed the enriched ketogenesis induced by the linoleic acid pathways (p = 0.017, topology value = 1), which is supported by blood and histomorphometric phenotypes. The above results indicate the foreseeable liver metabolic disorders when RS is fed to cows. These findings provide new insights into the liver metabolic mechanism and into crop by-products utilization using integrative omics technologies.