ghyslaine ppt

Animal Breeding & Genomics Centre

Gene detection for milk protein composit ion in dairy

cattleGhyslaine Schopen

Thursday 12th March 2009


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)


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


Heritabilities for milk protein composition

Ranged from 0.25 for β-casein to 0.80 forβ-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


Aim

To detect DNA regions on the cattle genome which have an effect on a quantitative trait


Resource population

873 cows

50 bulls

5 bulls

848 cows


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

BS

A 5

614

1B

SA 1

14

80 2

3

42

4 3

a-la

c 9

430

1 4

b-L

g-B 2

13

051 5

b-L

g-A

1

50

588 6

1

80

00 7

6

57

7 8

7

75

5 9

1

16

39 1

0

1

37

34

11

2

89

72 1

2

4

38

67 1

3

a-C

as-S

2 1

43

20

9 1

4

61

673

15

1

22

40

3 16

1

716

21 1

7

2

22

88

0 18

a-C

as-S

1 12

97

19

8 19

3

36

30 2

0 3

98

04 2

1

a-C

as-S

0 5

301

53 2

2

3

43

83 2

3 3

82

13 2

4

k-C

as 2

58

19

1 2

5 5

74

32 2

6

b-C

as-B 5

11

23 2

7

1

01

99

5 28

b-C

as-A

1 1

092

82

7 2

9

8

65

9 3

0

b-C

as-A

2 1

07

15

99 3

1 1

30

83

8 3

2

7

47

6 3

3 1

15

43 3

4 1

17

67 3

5

2

39

53 3

6 3

38

24 3

7

3

11

27 3

8 1

29

75 3

9

2

12

4 4

0

3

17

03 4

1

9

50

7 4

2

21

343

43

2

924

8 4

4

27

57

7 4

5

PDA - 214nm11891

NameAreaPk #


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


Variation between cows

Trait Mean

CV(%)

αs1-Casein 33.62 5

αs2-Casein 10.38 14

-Caseinβ 27.17 6

-Caseinк 4.03 14

-Lactoglobulin β 8.35 14

-Lactalbuminα 2.44 13

Caseinindex 87.45 2

Protein % 3.51 9

β-lactoglobulin

Num

ber

of o

bser

vatio

ns

% 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


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


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


Detected DNA region on chromosome 6 and 11

β-casein

0

1

2

3

4

5

0 20 40 60 80 100 120cM

Tes

t-st

atis

tics

к-casein

0

2

4

6

8

10

12

14

0 20 40 60 80 100 120cM

Tes

t-st

atis

tics

β-lactoglobul in

0

10

20

30

40

50

60

70

0 20 40 60 80 100 120cM

Tes

t-st

atis

tics


Detection of DNA regions

Correct for known candidate genes e.g. β-casein, к-casein and β-lactoglobulin


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

Nu

mb

er o

f o

bse

rvat

ion

s


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

Nu

mb

er o

f o

bse

rvat

ion

s Total

AA


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

Nu

mb

er o

f o

bse

rvat

ion

s

Total

AB


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

Nu

mb

er o

f o

bse

rvat

ion

s

Total

BB


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

Nu

mb

er o

f o

bse

rvat

ion

s

BB: 6.58%

AB: 8.16%

AA: 9.52%


Detected region on chromosome 11

β-LG

β-lactoglobulin

010203040506070

0 20 40 60 80 100 120

cM

Te

st s

tati

sti

c

β-LG


Detected DNA region on chromosome 6

β-casein

0

1

2

3

4

5

0 20 40 60 80 100 120cM

Tes

t-st

atis

tics

к-casein

0

2

4

6

8

10

12

14

0 20 40 60 80 100 120

cM

Tes

t-st

atis

tics

Casein

Casein


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


Opportunities for genetic selection

Cheese production (high casein%)

Health Promoting (low

fat %)


Acknowledgements

Farmers Partners:

Milk Genomics Team www.milkgenomics.nl


Thank You for your attention!

With breeding it is possible to change the milk protein composition!!

ghyslaine ppt

Engineering

casein whey proteins

casein fractions chromosome

major milk proteins

lactoglobulin lactalbumin

genetic markersind

lactoglobulin schopen

ttt tggctattct genetic

dairy cattleghyslaine