Analysis of the Milk Transcriptome using RNA Sequencing

A detailed analysis of the bovine milk transcriptome was performed on milk somatic cells collected at days 15, 90 and 250 of lactation in Holstein cows using RNA sequencing (RNA-Seq). A global analysis of gene expression was conducted across the lactation period and a more detailed analysis was done of glycosylation related genes, milk proteases and genes encoding enzymes in the citrate synthesis pathway. Analysis revealed that 61-69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk. Compared with the other two stages, transition milk (15d) showed less complexity in the transcriptome. The majority of the genes (~9,000) in milk were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome represented genes devoted to specific functions unique to the lactation stage. Ninety-two glycosylation-related genes were expressed in milk somatic cells. Most of these genes exhibited higher expression in day 250 samples, indicating an increase in net glycosylation-related metabolism.  A high throughput SNP discovery was performed in 14 RNA-seq libraries of milk and mammary tissues consisting of 259 million 40bp reads. A total of  160,873 SNP were found in 14 Holstein samples and 66.8% of them were heterozygous within the breed. Comparison of reference position to the bovine dbSNP database validated 63% of RNA-Seq detected SNP. Results of this study provided a valuable insight into the biology of lactation in the cow, as well as presenting many avenues for future research on the bovine lactome.