The project constitutes a Danish/Swedish initiative within the area of ”Milk genomics”. The main content of the project is to identify genetically contingent differences in the nutritional, technological and health-related properties of milk. By use of new “omics” techniques (genomics, metabonomics, proteomics) the genetic variation of the cow will be associated with detailed studies of the milk composition. Furthermore through sequencing of candidate genes for important components in milk, new markers for significant properties of milk are identified.
The long-term aim of the project is thus to identify gene markers to support development of future differentiated milk types of a high specific quality through breeding management
The initiative was established in spring 2009 and will run for 4 years.
Fig. 1. Figur of analyses on selections of milk and blood samples.
Project plan - WP's
WP1. Sampling and implementation of analysis methods
Selection of qualified herds based on pedigrees over descent of unrelated bull sires within the breeds Danish Holstein Friesians (SDM) and Jersey in Denmark. 400 milk and blood samples are taken from each breed. A parallel set of samples are taken in Sweden from Swedish Red Boskap (SRB) and Swedish Holstein (SLB). Proteomic methods involving protein profiling and MS detection of proteins and protein fosforylations and glycosylations are implemented (LC-MS, LC Q-TOF, MALDI MS/MS).
WP2. Characterisation of milk composition and functional properties
The overall composition – protein, fat, lactose, cell count, bacterial count, pH – is determined, and the yield is recorded. Furthermore selected technological (coagulation) and nutritional and health-related properties (fatty acid composition) are determined for all samples together with metabonomics by NMR to analyze small components and metabolites.
WP3. Genome scan and linkage with milk properties
Based on WP2, one of the four breeds is selected for a genome scan. This includes typing of gene markers in each of the 400 animals and subsequently heritability and global association studies are performed to quantify as well as locate that part of the genetic variation which associates with the composition and functional and other properties of the milk. Genotyping will be performed using af bovine 600K SNP-chip and Infinium technology (Illumina).
WP4. Genotyping of known and unknown milk protein variants and sequencing of candidate genes
Genotypes for the most important of the known casein variants (b- and k-casein) and for the most important of the known whey protein variants are determined using blood samples. Furthermore gene sequencing is carried out for candidate genes which are potentially affecting the milk properties measured.
WP5. Identification of correlations between proteomic results and functionality of milk
On the selection of the samples from WP2, detailed protein and peptide profiles are determined by proteomics and peptidomics. Storages characteristics and variations in protein modifications and other parameters are analysed on a small number of milk samples.
WP6. In vitro bioassays for evaluation of the effect of different protein polymorphisms on protein expression in intestinal cells
The global response of intestinal cells to treatment with different genetic types of milk is analyzed by an explorative approach involving metabonomic characterization of the cellular respons to identify key markers for response. Based on different protein and metabolic expressions, these proteins are identified by means of mass spectrometry for prediction of how the different milk fractions affect the metabolism and protein expression of the cells.
