The document summarizes research detecting DNA regions associated with milk protein composition in dairy cattle. The study identified regions on chromosomes 6 and 11 that influence casein and beta-lactoglobulin levels. The chromosome 6 region affected all four casein fractions and explained some genetic variants in casein genes. The chromosome 11 region influenced beta-lactoglobulin levels and explained variants of the beta-lactoglobulin gene. Identifying these DNA regions provides opportunities to use genetic selection to improve milk quality and composition for cheese and other dairy products.

1. Animal Breeding &
Genomics Centre
Gene detection for milk
protein composition in dairy
cattle
Ghyslaine Schopen
Thursday 12th
March 2009

2. Animal Breeding &
Genomics Centre
Milk Genomics Initiative
Aim: To identify opportunities to use genetic variation
to improve milk quality characteristics
 Milk quality:
 Milk-fat composition
 Milk-protein composition
 Improve:
 Technological efficiency (production of cheese, butter)
 Innovative dairy products (e.g. promoting human health)

3. Animal Breeding &
Genomics Centre
Milk composition
 Cow milk contains a unique source of bio-active
components and nutrient, among which proteins
 Six major milk proteins:
 Caseins: αS1-casein, αS2-casein, β-casein and к-casein
 Whey proteins: α-lactalbumin and β-lactoglobulin
 Milk protein composition is important for the dairy
industry:
 Caseins are important for the cheese production

4. Animal Breeding &
Genomics Centre
Heritabilities for milk protein composition
 Ranged from 0.25 for β-casein to 0.80 for
β-lactoglobulin Schopen et al 2009 Journal of Dairy Science
 Genes contribute to the genetic variation,
however, it is not known which genes cause the
genetic variation

5. Animal Breeding &
Genomics Centre
Aim
To detect DNA regions on the cattle genome which
have an effect on a quantitative trait

6. Animal Breeding &
Genomics Centre
Resource population
873 cows
50 bulls
5 bulls
848 cows

7. Animal Breeding &
Genomics Centre
Material & Methods
 Milk sample
 Capillary zone electrophoresis
 Blood sample
 DNA analyses
• 1912
• 398
• Pedigree
• 1
• Winter
• 1
Minutes
-6 -4 -2 0 2 4 6 8 10 12 14 16 18 20 22
AU
0.00
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
0.09
AU
0.00
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
0.09
BSA56141
BSA114802
34243
a-lac943014
b-Lg-B2130515b-Lg-A1505886
1800076577877559
1163910
1373411
2897212
4386713
a-Cas-S2143209146167315
12240316
17162117
22288018
a-Cas-S1129719819
3363020
3980421
a-Cas-S053015322
34383233821324
k-Cas25819125
5743226
b-Cas-B5112327
10199528
b-Cas-A1109282729
865930
b-Cas-A2107159931
13083832
747633
1154334
1176735
2395336
3382437
3112738
1297539
212440
3170341
950742
2134343
2924844
2757745
PDA- 214nm
11891
Name
Area
Pk #

8. Animal Breeding &
Genomics Centre
Detection of DNA regions
 Using 1341 Single Nucleotide Polymorphisms
(SNPs) as genetic markers
Ind 1 CACCGCGCCT GGTCCC G TTT TGGCTATTCT
CACCGCGCCT GGTCCC G TTT TGGCTATTCT
Ind 2 CACCGCGCCT GGTCCC A TTT TGGCTATTCT
CACCGCGCCT GGTCCC A TTT TGGCTATTCT
 Genetic markers can be used to reconstruct the
inheritance from parents to offspring

9. Animal Breeding &
Genomics Centre

10. Animal Breeding &
Genomics Centre
Variation between cows
Trait Mean
CV(
%
)
αs1
-Casein 33.62 5
αs2
-Casein 10.38 14
-Caseinβ 27.17 6
-Caseinк 4.03 14
-Lactoglobulinβ 8.35 14
-Lactalbuminα 2.44 13
Caseinindex 87.45 2
Protein % 3.51 9
β-lactoglobulin
Numberofobservations
% total protein
Caseinindex = (αs1-Casein + αs2-Casein +β-Casein + к-Casein) / (αs1-Casein + αs2-Casein +β-
Casein + к-Casein + β-Lactoglobulin + α-Lactalbumin) * 100
Schopen et al. (2009) Journal of Diary Science

11. Animal Breeding &
Genomics Centre
Detected DNA regions on the genome
 Significant regions (Pgenome< 0.05) at chromosome 1, 3, 5,
6, 9, 10, 11, 14, 15 en 17
 Chromosome 6: region affected all four casein
fractions
 Chromosome 11: region affected β-lactoglobulin
fraction

12. Animal Breeding &
Genomics Centre
Variance explained by DNA regions
Chromosome Trait VQTL
(%)
6 αS1
-casein 6.8
6 αS2
-casein 6.7
6 -caseinβ 3.6
6 -caseinк 7.9
11 -lactoglobulinβ 28.3

13. Animal Breeding &
Genomics Centre
Detected DNA region on chromosome 6 and
11
β-casein
0
1
2
3
4
5
0 20 40 60 80 100 120
cM
Test-statistics
к-casein
0
2
4
6
8
10
12
14
0 20 40 60 80 100 120
cM
Test-statistics
β-lactoglobulin
0
10
20
30
40
50
60
70
0 20 40 60 80 100 120
cM
Test-statistics

14. Animal Breeding &
Genomics Centre
Detection of DNA regions
 Correct for known candidate genes
 e.g. β-casein, к-casein and β-lactoglobulin

15. Animal Breeding &
Genomics Centre
β -lactoglobulin
0
20
40
60
80
100
120
140
160
180
4.0% 4.8% 5.6% 6.4% 7.2% 8.0% 8.8% 9.6% 10.4% 11.2% 12.0% 12.8%
% of total protein
Numberofobservations

16. Animal Breeding &
Genomics Centre
β -lactoglobulin
0
20
40
60
80
100
120
140
160
180
4.0% 4.8% 5.6% 6.4% 7.2% 8.0% 8.8% 9.6% 10.4% 11.2% 12.0% 12.8%
% of total protein
Numberofobservations
Total
AA

17. Animal Breeding &
Genomics Centre
β -lactoglobulin
0
20
40
60
80
100
120
140
160
180
4.0% 4.8% 5.6% 6.4% 7.2% 8.0% 8.8% 9.6% 10.4% 11.2% 12.0% 12.8%
% of total protein
Numberofobservations
Total
AB

18. Animal Breeding &
Genomics Centre
β -lactoglobulin
0
20
40
60
80
100
120
140
160
180
4.0% 4.8% 5.6% 6.4% 7.2% 8.0% 8.8% 9.6% 10.4% 11.2% 12.0% 12.8%
% of total protein
Numberofobservations
Total
BB

19. Animal Breeding &
Genomics Centre
β -lactoglobulin
0
20
40
60
80
100
120
140
160
4.0% 4.8% 5.6% 6.4% 7.2% 8.0% 8.8% 9.6% 10.4% 11.2% 12.0% 12.8%
% of total protein
Numberofobservations
BB: 6.58%
AB: 8.16%
AA: 9.52%

20. Animal Breeding &
Genomics Centre
Detected region on chromosome 11
β-LG
β-lactoglobulin
0
10
20
30
40
50
60
70
0 20 40 60 80 100 120
cM
Teststatistic
β-LG

21. Animal Breeding &
Genomics Centre
Detected DNA region on chromosome 6
β-casein
0
1
2
3
4
5
0 20 40 60 80 100 120
cM
Test-statistics
к-casein
0
2
4
6
8
10
12
14
0 20 40 60 80 100 120
cM
Test-statistics
Casein
Casein

22. Animal Breeding &
Genomics Centre
Conclusion
 Detected DNA region on chromosome 6 and 11
which affected the milk protein composition
 The DNA region on chromosome 6 affected all four
casein fractions and was partially explained by the
genetic variants in the casein genes
 The DNA region on chrosomsome 11 affected β-
lactoglobulin fraction and was partially explained
by the genetic variant A and B in β-lactoglobulin

23. Animal Breeding &
Genomics Centre
Opportunities for genetic selection
Cheese production
(high casein%)
Health
Promoting (low
fat %)

24. Animal Breeding &
Genomics Centre
Acknowledgements
 Farmers
 Partners:
 Milk Genomics Team
 www.milkgenomics.nl

25. Animal Breeding &
Genomics Centre
Thank You for your attention!
With breeding it is possible to change the milk
protein composition!!