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 in the Dutch Milk Genomics Initiative 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.

population

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).

 composition

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).

illumina

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.

 

Genetic parameters for milk urea nitrogen in relation to milk production traits. W.M. Stoop, H. Bovenhuis and J.A.M. van Arendonk (2007) Journal of Dairy Science 90: 1981–1986.Genetic parameters for major milk fatty acids and milk production
traits of Dutch Holstein-Friesians.
W.M. Stoop,
J.A.M. van Arendonk, J.M.L. Heck, H.J.F. van Valenberg and H. Bovenhuis (2008)
Journal of Dairy Science 91:  385-394.Characterization of milk fatty acids based on genetic and herd
parameters
.
J.M.L. Heck,  H.J.F. van Valenberg, H. Bovenhuis, J.
Dijkstra and A.C.M. van Hooijdonk (2011) Journal
of Dairy Research
.Genetic parameters for major milk proteins in Dutch
Holstein-Friesians
.
G.C.B. Schopen, J.M.L. Heck, H.
Bovenhuis, M.H.P.W. Visker,  H.J.F. van
Valenberg and J.A.M. van Arendonk (2009) Journal of Dairy Science 92:
1182-1191.Genetic and nongenetic variation in concentration of selenium,
calcium, potassium, zinc, magnesium, and phosphorus in milk of Dutch
Holstein-Friesian cows.
K.J.E. van Hulzen, R.C. Sprong, R. van der Meer
and J.A.M. van Arendonk (2009) Journal of Dairy Science 92: 5754–5759.

Genetic variation of natural antibodies in milk of Dutch
Holstein-Friesian cows
.
T.C.W. Ploegaert, S. Wijga,
E. Tijhaar, J.J. van der Poel, T.J.G.M. Lam, H.F.J. Savelkoul, H.K. Parmentier
and J.A.M. van Arendonk (2010) Journal of Dairy Science 93: 5467-5473.

 

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.

 

DGAT1 underlies large genetic variation in milk-fat composition of
dairy cows.
A. Schennink, W.M. Stoop, M.H.P.W.
Visker, J.M.L. Heck, H. Bovenhuis, J.J. van der Poel, H.J.F. van Valenberg and
J.A.M. van Arendonk (2007) Animal
Genetics 38
: 467-473.Milk fatty acid unsaturation: genetic parameters and effects of
Stearoyl-CoA Desaturase (SCD1) and Acyl CoA: Diacylglycerol Acyltransferase 1
(DGAT1).
A. Schennink, J.M.L. Heck, H. Bovenhuis,
M.H.P.W. Visker, H.J.F. van Valenberg and J.A.M. van Arendonk (2008) Journal of Dairy Science 91: 2135-2143.Effects of milk fat composition, DGAT1, and SCD1 on fertility traits
in Dutch Holstein cattle.
R.M. Demeter, G.C.B.
Schopen, A.G.J.M. Oude Lansink, M.P.M. Meuwissen and J.A.M. van Arendonk (2009)
Journal of Dairy Science 92:
5720–5729.Effect of polymorphisms in the FASN, OLR1, PPARGC1A, PRL and STAT5A
genes on bovine milk-fat composition.
A. Schennink, H. Bovenhuis, K.M. Léon-Kloosterziel,
J.A.M. van Arendonk and M.H.P.W. Visker (2009) Animal Genetics 40: 909-916.Novel polymorphisms in the bovine β-lactoglobulin gene and
their effects on
β-lactoglobulin protein concentration in milk. N.A. Ganai, H. Bovenhuis, J.A.M. van Arendonk and M.H.P.W. Visker
(2009) Animal Genetics 40: 127-133.

Effects of milk protein variants on the protein composition of
bovine milk.
J.M.L. Heck, A. Schennink, H.J.F. van
Valenberg, H. Bovenhuis, M.H.P.W. Visker, J.A.M. van Arendonk and A.C.M. van
Hooijdonk (2009) Journal of Dairy Science
92
: 1192-1202.

Relationships between milk protein composition, milk protein
variants, and cow fertility traits in Dutch Holstein-Friesian cattle.
R.M. Demeter, K. Markiewicz, J.A.M. van Arendonk and H. Bovenhuis
(2010) Journal of Dairy Science 93:
5495-5502.

Association of bovine β-casein protein variant I with milk
production and milk protein composition.
M.H.P.W.
Visker, B.W. Dibbits, S.M. Kinders, H.J.F. van Valenberg, J.A.M. van Arendonk
and H. Bovenhuis (2011) Animal Genetics
42
: 212-218.

 

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 scan for bovine milk-fat composition I. Quantitative
trait loci for short- and medium-chain fatty acids
.
W.M. Stoop, A.
Schennink, M.H.P.W. Visker, E. Mullaart, J.A.M. van Arendonk and H. Bovenhuis
(2009) Journal of Dairy Science 92:
4664-4675.Genome-wide scan for bovine milk-fat composition II. Quantitative
trait loci for long-chain fatty acids
.
A.
Schennink, W.M. Stoop, M.H.P.W. Visker, J.J. van der Poel, H. Bovenhuis and
J.A.M. van Arendonk (2009) Journal of
Dairy Science 92
: 4676-4682.Whole genome scan to detect quantitative trait loci for bovine milk
protein composition
.
G.C.B. Schopen, P.D. Koks,
J.A.M. van Arendonk, H. Bovenhuis and M.H.P.W. Visker (2009) Animal Genetics 40: 524-537.Genome-wide scan to detect quantitative trait loci for milk urea
nitrogen in Dutch Holstein-Friesian cows
.
A.C.
Bouwman, G.C.B. Schopen, H. Bovenhuis, M.H.P.W. Visker and J.A.M. van Arendonk
(2010) Journal of Dairy Science 93:
3310-3319.

 

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.

 

Genome-wide association of milk fatty acids in Dutch dairy cattle. A.C. Bouwman, H. Bovenhuis, M.H.P.W. Visker and J.A.M. van Arendonk
(2011) BMC Genetics 12: 43.Whole-genome association study for milk protein composition in dairy
cattle
.
G.C.B. Schopen, M.H.P.W. Visker, P.D. Koks,
E. Mullaart, J.A.M. van Arendonk and H. Bovenhuis (2011) Journal of Dairy Science 94: 3148-3158.

 

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.

 

Predicting bovine milk fat composition using infrared spectroscopy based
on milk samples collected in winter and summer
.

M.J.M. Rutten, H. Bovenhuis, K.A. Hettinga, H.J.F. van Valenberg and J.A.M. van
Arendonk (2009) Journal of Dairy Science
92
: 6202-6209.The effect of the number of observations used for Fourier transform
infrared model calibration for bovine milk fat composition on the estimated
genetic parameters of the predicted data
.
M.J.M.
Rutten, H. Bovenhuis and J.A.M. van Arendonk (2010) Journal of Dairy Science 93: 4872-4882.Prediction of β-lactoglobulin genotypes based on milk Fourier
transform infrared spectra
.
M.J.M. Rutten, H.
Bovenhuis, J.M.L. Heck and J.A.M. van Arendonk (2011) Journal of Dairy Science 94: 4183-4188.Predicting bovine milk protein composition based on Fourier
transform infrared spectra
.
M.J.M. Rutten, H.
Bovenhuis, J.M.L. Heck and J.A.M. van Arendonk (2011) Journal of Dairy Science 94: 5683-5690.

 

Future
research and collaboration

Further analyses on e.g. milk-fat
composition, mineral composition and minor proteins are in progress. It
is very well possible that the data can be of value also for other research
groups for use in other types of analyses. We welcome further and alternative
use of our data. When you are interested, please use the IMGC portal to contact
the Dutch Milk Genomics Initiative to arrange the exchange of data.

 

Initiatives similar to the Dutch Milk
Genomics Initiative have started in France and in Scandinavia. The French
PhénoFinLait is collecting data on 12,000 cows, 4000 ewes and 4000 goats, while
the Danish-Swedish Milk Genomics Initiative is collecting data on 1200 cows. It
is anticipated that, in due time, data of these initiatives will also become
available for exchange.

 

Acknowledgement

The Dutch Milk Genomics Initiative is a collaboration between the Dairy Science and Technology Group and the Animal Breeding and Genomics Centre of Wageningen University, and is financially supported by Wageningen University, the Dutch Dairy Association (NZO), Cooperative Cattle Improvement organization CRV and the Dutch Technology Foundation STW.