Whole Genome Scan:QTL for Milk Fat Composition in Summer Wageningen university

1. Animal Breeding &
Genomics Centre
Whole Genome Scan:
QTL for Milk Fat Composition in
Summer
Nazir A Ganai
Tuesday 24th
March 2009

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

3. Animal Breeding &
Genomics Centre
Milk Fat composition
 Importance
Major energy component - 2.25 times caloric value of CHOs
Farmers: for economics
Industry: for quality dairy products
Designer Milk: for good health
An (indirect) aim of the Milk Genomics Initiative
MGI aims to find the QTL / genes underlying the variation of milk fat
composition
Ultimately propose genetic interventions to alter the milk fat composition for
good health and/or better processing qualities

4. Animal Breeding &
Genomics Centre
Human versus Cow milk composition
Constituent Human
milk
Cow milk
Protein % protein 1.3 % 3.5%
Casein : Whey protein 40:60 80:20
Fat % fat 3.9% 4.0%
Saturated 1.8 g/100g 2.5
Mono-Unsaturated 1.6 1.0
Poly-unsaturated 0.5 0.18

5. Animal Breeding &
Genomics Centre
Milk Fat Composition
Normal Milk
 Fat % 3 to 5%
 SFA ~68%
 MUFA ~27%
 PUFA ~5%
Ideal milk
 Fat % ~2%
 SFA < 8%
 MUFA 82%
 PUFA 10%

6. Animal Breeding &
Genomics Centre
Milk Fatty acids and human health
Type of Fat Role Effect
Sat. Fatty Acids Lauric acid (12:0)
Palmitic acid 16:0
Myristic acid
Raise LDL Cholestrol
•Atheroseclerosis
•High BP
•CHD
Trans fatty acids Trans 18:1
Unsat. Fatty
acids
Oleic acid cis 18:1
Linoleic acid 18:2
Linolenic acid 18:3
Lower LDL Cholestrol Good for health

7. Animal Breeding &
Genomics Centre
Milk Fat Profile
• 400 different FA in milk
• Different ways to classify
•Origin in Milk
•Short / Medium Chain: synthesized de novo
•Long Chain : preformed-
•Melting point:
•Saturated
•Un saturated
•Biological properties
•Good for health
•Bad

8. Animal Breeding &
Genomics Centre
 SFA ~68%
 MUFA~27%
 PUFA ~5%
C4:0 to C20:0
C14:0 = ~12%
C16:0 = ~30% Palmitic acid
C18:0 = ~10%
C10:1 to C18:1
C18:1cis9 = ~21%
C18:1trans = ~2.15%
C16:1 = ~1.4%
C14:1 = ~1.16%
C18:2 cis9,12 (Linoleic acid) 1.12
CLA cis9, trans11(C18:2) Rumenic acid 0.56
C18:3 cis9,12,15 α-Linolenic acid 0.50
Fatty Acid Profile

9. Animal Breeding &
Genomics Centre
Variability in milk fat composition
 Environmental:
 FA profile highly sensitive to the kind of feed
 Summer milk fat – low in saturated, high in unsaturated
Trait Summer Winter
UFA 29.24 25.5
C18trans 2.14 1.50
CLAcis 9, tr 11 0.56 0.39
C18:3 cis9,12,15 0.50 0.41
C16:0 29.0 32.6

10. Animal Breeding &
Genomics Centre
Heritability
 Short and medium chain 0.23 to 0.57
 Long chain FA 0.12 to 0.33
 Genes involved in biosynthesis of milk : > 40
 To find genes causing genetic variation :
difficult
 Therefore, the first approach to is find QTL
underlying the genetic variation

11. Animal Breeding &
Genomics Centre
Aim
 To find QTL for milk fat composition in summer
 Compare the results with winter milk fat analysis

12. Animal Breeding &
Genomics Centre
Material & Methods
• Resource population
• 1905 Cows
• 398 herds
• 7-sire families
• Milk sampling
• Summer
• Marker Map: 1341 SNPs over 29 autosomes
• Analysis: Multi-marker regression analysis

13. Animal Breeding &
Genomics Centre
Genome Scan Results
 Total fat Traits: 46
 Significant QTL (PGenome <0.05) : 4
 BTA14, BTA15, BTA26, BTA27
 Variation explained in: 33 traits
 Suggestive QTL: 20
 Variation explained in: 44 traits

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

15. 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 #

16. 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

17. Animal Breeding &
Genomics Centre

18. Animal Breeding &
Genomics Centre
BTA-14: Long Chain Fatty Acids
0
5
10
15
20
1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101
cM
Fvalue
0
0.25
0.5
0.75
1
InformationContent
C18:1
C18:1cis9
C18:2
C18:2 cis9,12
c183
fat%
ratio SFA/UFA
SFA
Total index
UFA
IC
BTA-14: Medium & Shrot Chain FA
0
2
4
6
8
10
12
14
16
18
1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 76 81 86 91 96 101
cM
Fvalue
0
0.25
0.5
0.75
1
InformationContent
C7:0
C9:0
C11:0
C13:0
C16:0
C16:1
IC

19. Animal Breeding &
Genomics Centre
BTA 26: QTL at 28 cM for Mono-unsaturated Fatty Acids
0
5
10
15
1 11 21 31 41 51 61
Fvalue
0
0.25
0.5
0.75
1
InformationContent
C10:1
C14:1
C16:1
C10index
C12index
C14index
C16index
IC

20. Animal Breeding &
Genomics Centre
Variance explained by DNA regions
Chromosome Trait VQTL
(%)
14 Fat% 12
SFA 9.2
UFA 8.7
FA 3 - 10%
26
27
MUFA
C5:0, C11:0
1 – 4%
1.3 – 1.8%

21. Animal Breeding &
Genomics Centre
Comparison between results on summer & winter
samples
#BTA Position Summer Fat Winter Fat
6 - - C6:0, C8:0
14 0 cM 24 traits 21 traits : same
Exceptions: C6:0, C8:0, C10:0
15 38 cM
9 cM
C4:0
C17:0
C18:1 trans
16 - - C18index
CLAindex
19 - - C14:0
26 28 cM MUFA MUFA
27 6 cM Odd Chain FA
C5 : C13
-

22. Animal Breeding &
Genomics Centre
Comparison for individual FA
Trait rA
Chromosomes with QTL
Winter Summer
fat% 0.97 6,8,11,13,14,27 5,7,8,13,14
C4:0 0.95 2,7,19,25,27 15,18
C6:0 0.94 2,6,13,23 13,14,15
C8:0 0.94 6,14,17,29 13,14
C14:0 0.93 14,19,22,26 15,21,29
C16:0 0.78 1,4,6,9,11,14 5,14,19,24
C18:0 0.84 1,11,16,19 8,11,21,23
C18:1 cis 9 14,21 14,24,28
C16:1 1,6,13,14,19,26, 14,15,18,26,
C14:1 26,13,19 8,11,15,26
C18:2 cis 9,12 0.96 7,11,12,14 14
CLA cis9, trans 11 0.82 11,14,17 14,29
C18:3 cis9,12,15 0.83 3,14,22 9,11,14,21

23. Animal Breeding &
Genomics Centre
Conclusion (for summer milk fat)
 Detected 4 QTL on BTA14, 15, 26 and 27 for summer milk fat
composition.
 QTL on BTA14 significantly influenced most of the traits, both saturated
and unsaturated.
 QTL on BTA15 influenced the saturated FA only (C4:0 and C17:0).
 QTL on BTA26 specifically influenced MUFA. The source of such FA
in milk is the desaturation activity of enzyme SCD, for which the gene
has been already mapped to BTA26.
 QTL on BTA27 specifically influenced odd-chain Saturated FA.
The origin of such FA is different from even-chain FA.

24. Animal Breeding &
Genomics Centre
Summer vs Winter milk fat composition
 Similarities:
 Only two QTL on BTA14 and BTA26 influence the same traits in both
seasons.
 Differences:
 3 QTL on BTA6, 16, 29 influenced fat composition in winter milk only.
 QTL on BTA27 is influenced fat composition in Summer milk only.
 All the suggestive QTL on 23 other autosomes influenced different traits
in two seasons.
 This lack of consistency :
 background effects like : epistasis and environmental
interactions,
 less powerful experimental design (half-sib structure) for QTL analysis.

25. Animal Breeding &
Genomics Centre
Opportunities for genetic selection
Health Promoting
(low fat %)I beleive there is a
long way before we
can modulate the
milk fat composition
for a Designer Milk
through marker
assisted selection !!

26. Animal Breeding &
Genomics Centre
Thank You for your attention!