Wickramasinghe et al. BMC Genomics 2012, 13:45 http://www.biomedcentral.com/1471-2164/13/45 R E S E A R C H A R T I C L E Transcriptional profiling of bovine milk using RNA sequencing Saumya Wickramasinghe, Gonzalo Rincon, Alma Islas-Trejo and Juan F Medrano* Open Access Abstract Background: Cow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells. Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. Gene Ontology (GO) and pathway analysis were performed using the Blast2GO program and GeneGo application of MetaCore program. Results: A total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation. Conclusions: This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome. Background Milk is a unique biological fluid consumed by mamma- lian infants. It contains many macro- and micro-nutri- ents that are essential for the growth and development of the newborn [1,2]. In addition, a diverse cocktail of bioactive factors, such as antibodies, oligosaccharides and nucleotides in milk, play immune, pre-biotic and protective functions in the infant gut [1,3,4]. Cow milk has an important role in human nutrition because cow milk-based infant formula is the most available substitute for human breast milk and cow milk is consumed beyond infancy in human populations * Correspondence: jfmedrano@ucdavis.edu Department of Animal Science, University of California Davis, CA, 95616- 8521, USA around the world. However, there are significant differ- ences between the physicochemical properties of human breast milk and cow milk [5]. Bovine milk contains a higher percentage of caseins whereas human milk has higher percentage of whey proteins, the highest being a- lactalbumin. b-lactoglobulin, the most abundant whey protein in bovine milk, is not present in human milk. These differences between human and cow milk in the amount and types of proteins have been suggested to be responsible for cow milk allergies in approximately 2- 2.5% of human infants [6]. Oligosaccharides are abun- dant in human milk, and studies on milk demonstrate local and systemic beneficial effects to the suckling neo- nate [7,8]. The concentration of free oligosaccharides in bovine milk is reported to be approximately 20-fold © 2012 Wickramasinghe et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.