UC Davis researchers are using RNA-seq technology and data analysis software from CLC Bio to develop a comprehensive description of the bovine milk and mammary gland transcriptome in lactating cows.
The results reveal that approximately 50 per cent of the annotated genes are expressed during lactation and that variations in gene expression exist at different stages of lactation as an adaptation to different molecular functions of milk according to the biological need of the animal.
'There is considerable interest in producing food products that have an enriched content of oligosaccharides, in order to create probiotic products that will have a benefit for human health - something our research can facilitate,' said Prof Juan F Medrano from the Department of Animal Science at UC Davis.
'For our RNA sequence analysis, it has been helpful to use CLC Bio's software to assemble the millions of reads against the bovine reference genome.
'That has helped us identify the level of expression of all the genes in the mammary epithelial cells, identify splice variants and efficiently determine real SNPs in our comparisons,' he added.
The researchers from UC Davis will publish a paper in 'Mammalian Genome' that demonstrates how analysing the milk-cell transcriptome using RNA-seq is an efficient and cost-effective method to identify SNPs in the transcribed regions.
This research will provide a collection of more than 30,000 SNPs located in coding regions of genes expressed during lactation that can be used for gene variation analysis and to examine the effect of genetic associations on milk-related traits in cattle.