Dissertation/Thesis Abstract

Trancriptome profiling of bovine milk with special emphasis on oligosaccharide metabolism genes
by Wickramasinghe, Saumya, Ph.D., University of California, Davis, 2011, 206; 3502360
Abstract (Summary)

Cow milk is a complex bioactive fluid consumed by humans beyond infancy. It contains many nutrients and a diverse cocktail of bioactive factors. 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 research project was designed to study the transcriptome of bovine milk somatic cells by RNA sequencing with a special emphasis on genes encoding enzymes in milk oligosaccharide metabolism.

First a detailed literature review was conducted on milk oligosaccharides and RNA sequencing (RNA-seq) technology (chapter 2). Next, RNA-seq was conducted on cDNA libraries constructed from milk somatic cells collected at days 15, 90 and 250 of lactation Holstein cows (chapter 3). In this chapter a global analysis was conducted on the bovine milk transcriptome. This was followed by a detailed analysis on the expression of genes encoding major milk components (lactose, protein, fat), proteases and genes in ubiquitin-proteasome pathway. In chapter 4 genes coding for enzymes involved in bovine milk oligosaccharide metabolism was examined by comparing the oligosaccharide profiles with the expressions of 121 glycosylation-related genes in milk somatic cells of Holstein and Jersey cows at days 15 and 250 of lactation. Finally, single nucleotide polymorphism (SNP) discovery analysis was performed on a larger group of Holstein cows (14 samples) consisting of RNA-Seq reads obtained from milk and mammary tissue cDNA libraries. Analysis was also performed in RNA-Seq reads obtained from milk cDNA libraries of Jersey, Shorthorn and Brown Swiss cows of smaller sample sizes. A detailed analysis was also conducted on the SNP detected on 121 glycosylation related genes (chapter 5).

Milk transcriptome analysis had shown the unique properties of milk and the ability of milk cells to adapt different molecular functions according to the biological need of the animal. Study on genes in bovine milk oligosaccharide metabolism provided considerable insight into bovine milk glycobiology and its underlying genetic mechanisms. The SNP profiling provided a valuable resource of thousands of coding SNP expressed in the milk and mammary gland of dairy cows. Results of this study herein provided a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome.

Indexing (document details)
Advisor: Medrano, Juan F.
Commitee: Famula, Thomas R., Oberbauer, Anita M.
School: University of California, Davis
Department: Animal Biology
School Location: United States -- California
Subjects: Genetics, Animal sciences
Keywords: Gene expression, Milk, Oligosaccharides, RNA sequencing, Single nucleotide polymorphisms
Publication Number: 3502360
ISBN: 9781267252845