yes en all home 20061031 Patrick pics/banners/17.jpg Dutch Milk Genomics Initiative The aim of the Dutch Milk Genomics Initiative is to identify genes that contribute to natural genetic variation in milk-quality traits, in particular milk-fat and milk-protein composition. The program provides tools for improved breeding programs to exploit natural genetic variation in milk-quality traits and contributes to the knowledge base needed for innovative dairy products. The Milk Genomics Initiative combines expertise in the fields of dairy science, quantitative genetics, genomics and bioinformatics. Population The work started in 2005 with the collection of milk samples and blood (for extraction of DNA) from a resource population of 2000 Dutch Holstein Friesian cows in their first lactation. Cows were on 400 commercial herds in the Netherlands and 5 cows per herd were sampled. This population has been designed for estimation of genetic parameters (such as heritabilities and genetic correlations) as well as for detection of Quantitative Trait Loci (QTL) and analysis of association. The population consists of 5 large half-sib families of 200 daughters per sire and 50 small half-sib families of 20 daughters per sire, and pedigree information of all cows is available. In addition to the biological samples we also collected information regarding cow health and herd practices. Milk samples Cows were milked twice a day and milk samples were taken in late winter (February - March), in spring (April - May) and in early summer (June - July) 2005. All biological samples are stored in our bio bank. The winter milk samples have been used for extensive phenotyping of detailed milk composition, resulting in information on milk production traits, fat composition, protein composition, mineral composition and titers for natural antibodies. In winter all cows were kept indoors. The summer milk sample has been used to determine fat composition. In summer about half of the cows had access to pasture for at least part of the day. Milk production traits (milk production, fat, protein and lactose concentration, fat, protein and lactose production, somatic cell count, urea, pH) were determined by infrared spectroscopy using a MilkoScan FT 6000 (Foss Electric, Denmark). Detailed milk-fat composition (up to 130 individual fatty acids) was determined by Gas Chromatography (GC). Detailed milk-protein composition (the 6 major milk proteins) was determined by Capillary Zone Electrophoresis (CZE). DNA Genomic DNA was isolated from the collected blood samples of the cows and from semen samples of their sires. This DNA has been used for several dedicated genotyping assays such as Taqman allelic discrimination and SNaPshot single base primer extension. The DNA has also been used for two genome-wide scans of 1500 and 50,000 SNP markers, respectively. Both sets of markers were custom-made. The set of 1500 SNP markers was genotyped with the Golden Gate assay (Illumina, USA) and the set of 50,000 SNP markers was genotyped with the Infinium assay (Illumina, USA). This unique, extensive set of phenotypes and DNA markers has been used for various genetic analyses. Heritabilities and genetic correlations Genetic parameters such as heritabilities and genetic correlations have been estimated for milk production traits, fat composition, protein composition, mineral composition and titers for natural antibodies. Most of these studies showed moderate to substantial genetic variation, implying opportunities for genetic selection. Candidate genes Polymorphisms in candidate genes have been studied for associations with milk-fat composition and milk-protein composition. These studies comprised polymorphisms that were known from previous research as well as polymorphisms that we detected by screening candidate genes. For a considerable number of traits these polymorphisms in candidate genes accounted for a substantial part of the genetic variation. Genome scans Linkage analysis using 1500 SNP markers for the 5 large half-sib families has been performed for milk-fat composition, milk-protein composition and milk urea nitrogen. QTL that were linked with various fatty acids were found on 6 different chromosomes and QTL that were linked with the major milk proteins were found on 3 different chromosomes. Genome-wide association using 50,000 SNP markers has been analysed for milk-fat composition and milk-protein composition. Highly significant associations with multiple fatty acids were found on chromosomes 14, 19 and 26. Highly significant associations with the 6 major milk proteins were found on chromosomes 5, 6 and 11. In addition, many regions were detected that showed less significant associations or associations with only a limited number of traits. Infrared spectroscopy Infrared spectroscopy is routinely used to determine milk production traits such as fat, protein and lactose concentrations. We have investigated whether infrared spectroscopy can also be applied to determine detailed milk-fat composition and milk-protein composition. This research shows that fatty acids that are present at reasonable quantities can be predicted accurately with infrared spectroscopy. The predictions at the phenotypic level of milk-protein composition were not very accurate. However, genetic correlations between infrared-predicted and CZE-determined protein composition were high, implying opportunities for application of infrared predictions in genetic selection. Future research Further analyses on e.g. milk-fat composition, mineral composition and minor proteins are in progress. International Milk Genomics Consortium We are proud to be member of the International Milk Genomics Consortium, which provides a collaborative, interactive and pre-competitive platform for researchers and industry to accelerate the understanding of the biological processes underlying mammalian milk genomics and facilitates the transition of that knowledge into usable benefits for producers, manufacturers and consumers of dairy products. extpage http://www.milkgenomics.org/ International Milk Genomics Consortium nl all home 20061113 Raoul pics/banners/17.jpg Milk Genomics Initiatief Genetische verbetering van melkkwaliteitseigenschappen, en productinnovatie Het doel van het Milk genomics initiatief is het vinden van de genen die bijdragen aan de natuurlijke genetische variatie van melkkwaliteitskenmerken, in het bijzonder waar het de melkvet- en melkeiwitsamenstelling betreft. Het project zal gereedschappen aanreiken voor verbetering van fokprogramma's om de natuurlijke variatie in melkkwaliteitskenmerken te benutten, en draagt bij aan de kennis die nodig is voor innovatie in zuivelproducten. Het Milk genomics initiatief combineert expertise op het gebied van zuivelkunde, kwantitatieve genetica, genomics en bio-informatica. Er zijn melkmonsters en bloedmonsters (voor DNA-extractie) genomen bij een populatie van 2000 Nederlandse Holstein Friesian koeien in hun eerste lactatie. Deze populatie is samengesteld voor de schatting van genetische parameters (zoals erfelijkheidsgraad en genetische correlaties) en voor de detectie van QTL. Alle biologische monsters zijn opgeslagen in onze biobank. De samenstelling van de melk is gedetailleerd gemeten, zodat er nu informatie is over standaard melkproductiedata (melk-, vet-, eiwit- en lactoseproductie; vet-, eiwit- en lactoseconcentratie, celgetal, ureum, pH), eiwitsamenstelling (alle belangrijke melkeiwitten inclusief genetische varianten), en vetsamenstelling (afzonderlijke vetzuren). Deze unieke, uitgebreide databank wordt nu gebruikt voor kwantitatief-genetische analyses om erfelijkheid en genetische correlaties vast te stellen. Een genoombrede scan met 1500 moleculaire merkers (SNP) is opgezet om chromosomale gebieden (QTL) te vinden die de melksamenstelling beïnvloeden. Vervolgens zal finemapping plaatsvinden voor een beperkt aantal QTL met gereedschap dat gebruik maakt van linkage disequilibrium-informatie. Toekomstplannen zijn het vinden van mogelijkheden voor differentiatie met behulp van merkers en merker-ondersteunde selectie voor het verbeteren van de kwaliteit van melk en de efficiëntie van melkproductie. Verder willen we de kwaliteit van zuivelproducten van dieren met extreme genotypes evalueren. De industriële partners van het Milk genomics initiatief garanderen het gebruik van de resultaten en verzekeren een snelle verspreiding van de relevante kennis naar de praktijk van de melkveehouderij en de innovatie van zuivelproducten. International Milk Genomics Consortium Wij zijn trots op onze deelname in het International Milk Genomics Consortium. Dit consortium voorziet in een platform voor samenwerking en interactie tussen onderzoekers en industrie, ter bevordering van het begrip van de biologische processen achter de genomics van zoogdiermelk. Daarnaast stimuleert het consortium de overdracht van die kennis zodat deze door producenten, fabrikanten en consumenten van zuivelproducten kan worden toegepast. extpage http://www.milkgenomics.org/ International Milk Genomics Consortium