Milking the genes: Genetic analysis of milk.
Juan Medrano, UC Davis
What is the perfect food? Milk. Lactation: 120 million years of evolution. The darwinian engine of nutrition.
Constituents of human milk. Not a homogenous mixture. 88% water, 12% solids. Zivkovic A M et al. PNAS 2011, 108 p4653-4658. Solids include 70g/L lactose, 40g/L lipids, 8g/L proteins, 5-15g/L Human Milk Oligosacharides. (Oligosaccharides vary between animals, etc.)
Overview of milk production. Mammary tissue sample not possible in human, but you can extract cells from milk itself.
High correlation between somatic cells and expression in mammary gland. [Must have missed something, not sure where that came from.]
RNA-seq technology overview. De novo, snp, indels, new transcripts. Pathway analysis and functional annotation.
Look at overlap between mammary specific genes (570), mammary and milk(11.6k), milk specific (1k). High correlation.
Milk transcriptome at different stages of lactation. Used cows, sample in three major periods: start of lactation, peak lactation and end of lactation. There is a skew in this. 10 genes represent 61% of reads at day 15, but only 11% on day 90.
Proteolytic enzymes in milk. Changes dramatically, increasing over course of 3 samples taken. Important in many processes, including cheese making. [yes, we’re still talking about cows.]
Milk microbiome also determined for bovine and human milk. there are beneficial bacteria in milk. In Human, apx 60 different strains – about 20 uncultured. In cow, about 2000 strains, 188 uncultured
Target validation. Pathway analysis also done. SNP selection. Marker trait association studies to identify regulators of the pathway in an experimental way.
One example of this is citrate in milk. It’s a buffer in milk, Ca and P balance. Heat stability, etc. 74 snps in 20 genes used for an association study. Citrate content in milk was measured in 350 Holstein and 200 Jersey cows. [how often do I get to write stuff like that? (-: Moooo.] worked well to identify a gene of interest.
- milk is interesting
- RNA-workflow is powerful and insightful
- Understanding expression patterns may help for future milk producers and users (bovine)
- microbiome can have significant impact on our health
- Pathway analysis can give us insight.