Liver RNA-seq expression analysis in cattle supplemented with rumen-protected choline

Abstract

Nutrition plays a major role in animal performance, while nutrigenomic studies how food affects gene expression. Several researches were done over feeding systems including diets, feedstuffs, essential nutrients, vitamins and cofactors. Within them, choline is a water-soluble essential nutrient that serves as methyl donor and cofactor; as a precursor of acetylcholine, phospholipids and betaina; required for growth, neural development and fat metabolism. Choline is de novo synthesized but a dietary intake is required, but in ruminants has been used as rumen-protected choline (RPC) as it is easily degraded in rumen. Despite its demonstrated metabolic effect, little is known about the regulation of gene expression in the liver of choline supplement in beef cattle. The objective of this study was to evaluate the differential gene expression and enriched pathways when adding RPC to the diet of fattening beef cattle. A total of 11 Braford steers were fed during 85 d with a formulated diet (89% DM, 15.1% CP, 31% NDF; 5.6% EE, 43.3% starch, 2.9 Mcal ME/kg DM), whereas 6 of them receive 6 g/animal/day of RPC. At slaughter, a liver sample was taken, preserved in RNA-later, and whole expression NGS sequencing was performed. Quality control of sequences, alignment to reference genome (UMD3.1) and raw count matrix data was conducted using FASTQC, hisat2, samtools and featureCounts softwares. Differential expression analysis was carried out by edgeR and DESeq2, R packages. DAViD, FAANG and Panther tools were used to get the Gene Ontology (GO) enriched terms. Results showed 945 genes with significantly modified expression (P < 0.05), and 13 of them remained after Holm-Bonferroni correction. The GO analysis identified terms related to the enhancement of immunity (innate immunity, T-cell activation and B cell receptor signaling pathway), cellular transportation (exosome, scavenger receptor activity and LDL transport), protein binding and collagen trimer. This agreed with several studies that showed an increment of immune response when choline is supplemented, and support the reported hepatic protection. Finally, could introduce information about the mechanism behind the liver fat reduction and enhanced milk production observed in dairy cattle.