ADSA®-EAAP speaker exchange presentation: Effect of rumen content exchange on gene expression in rumen epithelium of lactating cows

Abstract Text: The ruminal epithelium may adapt to changes in diet either by adjusting the absorptive capacity and surface area of papillae or through acute cellular functional adaptations. To test this hypothesis, an experiment involving total rumen content exchange between 3 pairs of lactating cows fed the same diet was performed to investigate the influence of variation in rumen contents and microbial populations therein on gene expression in rumen papillae. Papillae samples were taken during and 1 week after digesta exchange from the ventral sites of rumen. Sequencing libraries were prepared according to Illumina TruSeq® Stranded mRNA and TruSeq® Small RNA sample preparation. Paired-end sequencing with Illumina HiSeq3000 with 2 x 150 bp read length was used for mRNA (average 50.6 M reads per sample) and single-read sequencing with 1 x 50 bp read length for miRNA (average 2.5 M reads per sample). From mRNA 67.8% of reads were mapped, of which 53.5% were located to known genes, the remaining reads mapping to unannotated regions of the bovine genome. Each animal was analyzed for differential gene expression (DE) between the two time points using edgeR. The p-values of DE genes were used for hierarchical clustering to identify groups with different responses. Using this approach experimental animals (n=6) formed two clusters. DE analysis within the clusters revealed 170 genes differentially expressed at FDR<0.1 in cluster 1 and two genes differentially expressed in cluster 2. The gene set was analyzed with Ingenuity^®Pathway analysis (Qiagen). The top five affected canonical pathways were Acyl-CoA hydrolysis, xenobiotic metabolism signaling, dermatan sulfate biosynthesis, chrondroitin sulfate biosynthesis and IGF-1 signaling. Twelve phenotypes were significantly different between the two clusters before exchange (ANOVA, p<0.1 by permutation test), with cows in cluster 1 having higher milk protein content, lower total tract N digestibility, greater fecal N excretion, and higher molar acetate and lower valerate proportions in rumen VFA. From miRNA libraries 36.3% of reads were uniquely mapped. From 811 annotated miRNAs, 382 miRNAs were expressed. Analyses of miRNA expression between the two clusters revealed miRNAs with large differences before and after the exchange, five of which have been recently reported to be correlated with N efficiency in cows fed low quality forage diets. To conclude, the transfer of digesta contents was associated with alterations in the expression of key genes and gene networks in rumen epithelium.

Keywords: dairy cow, rumen epithelium, transcriptomics