1. S. Vanderick1,2, F.G. Colinet1, A. Mineur1, R.R Mota1,
Genetic parameters of novel mid-infrared predicted milk traits in three dual-purpose cattle breeds
S. Vanderick1,2, F.G. Colinet1, A. Mineur1, R.R Mota1,
N. Gengler1, H. Hammami1
1 Gembloux Agro-Bio Tech, ULiège, B-5030 Gembloux, Belgium 2
EAAP 2018 Meeting Dubrovnik

2. EAAP 2018 Meeting Dubrovnik
Dual-purpose cattle
Dual-purpose cattle in Europe play a very important role because one individual cow combines the two essential characteristics: production of milk and production of meat.
The main dual-purpose cattle breed in Walloon Region of Belgium is Dual-Purpose Belgian Blue, which is a local breed, but there are also MON and NOR animals.
Dual-purpose
Belgian Blue
(dpBB)
Montbéliarde
(MON)
Normande
(NOR)
EAAP 2018 Meeting Dubrovnik

3. EAAP 2018 Meeting Dubrovnik
Dual-purpose cattle
For breeding or management purposes, we need to collect relevant phenotypes in routine on a large-scale … but this can be a challenge especially for these small sized cattle populations, even more in organic farming which are pasture-based systems!
Costly
Not repeatedly collected even on-farm level
Difficulty in gathering relevant large-scale data in routine
Small sized cattle populations
(Organic) pasture based production systems
EAAP 2018 Meeting Dubrovnik

4. Usefulness of mid-infrared spectra (MIR)
Milk samples
(milk payment, milk recording)
Raw data = MIR spectra
Calibration equations
Quantification
wide range of novel phenotypes !
MIR analysis
FOSS
Since recently, mid-infrared spectrometry has been recognized as a rapid and cost-effective tool to collect routinely a wide range of accurate of milk-based biomarkers. Therefore, MIR can be also useful for dual-purpose cattle… in order to get accurate and relevant data which could be helpful for breeding and management purposes…
EAAP 2018 Meeting Dubrovnik

5. EAAP 2018 Meeting Dubrovnik
Objectives
Genetic parameters of 39 novel MIR predicted milk traits
How MIR traits can predict longevity at early stages?
Any help from genomics?
Our objective was three-fold,
First, genetic parameters of 39 novel MIR traits were estimated for each of the 3 dual-purpose cattle breeds.
Then, in the context of development of breeding programs for small sized populations, it was important to see how these novel MIR traits can be useful to assess longevity at early stages.
And finally, also in line with the topic of this session, we investigated how genomics can be helpful for the predictions of longevity with those novel MIR traits.
EAAP 2018 Meeting Dubrovnik

6. EAAP 2018 Meeting Dubrovnik
Data
dpBB
MON
NOR
Cows in production
2,988
1,330
621
1st lactation test-day
21,287
10,062
4,637
2nd lactation test-day
11,771
6,716
2,532
3rd lactation test-day
6,246
4,217
1,370
Pedigree
7,744
3,807
2,304
For the genetic parameters estimation, test-day records from the first-three lactations for the 3 breeds were used. As you can see, these data are limited with almost 3000 cows in production for the original national breed, about 1300 cows in production for MON and only 600 cows for NOR
EAAP 2018 Meeting Dubrovnik

7. MIR predicted milk traits
Cheese properties: 8
Groups of fatty acids (FA): 14
Minerals: 5
Protein components: 8
Ketone bodies: 3
Methane (CH4)
single-trait multi-lactation random regression
test-day model
Genetic parameters of the following MIR traits were computed within breed with a single-trait multi-lactation random regression test-day model.
Some of those traits are quite familiar – such as milk fatty acids, cheese technological properties or Methane – and others are less - minerals, ketone bodies…
Genetic parameters were also computed for conventional production traits (milk, fat, protein contents and % + SCS)
EAAP 2018 Meeting Dubrovnik

8. Conventional Production traits Cheese properties Ketone bodies
In this slide, results for average daily h² over the lactation of each trait are summarized (means through the first-three lactations of these average daily h² for each trait) . Breeds are differentiated by colours and shapes of symbols.
CH4
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

9. Conventional Production traits Cheese properties Ketone bodies
These values tended to be higher for dpBB ( ) than for MON and NOR ( ) breeds.
Some large differences between breeds have been observed… especially between dpBB and Normande breed for milk composition mainly.
CH4
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

10. Conventional Production traits Cheese properties Ketone bodies
The estimated values of h² for methane make sense with a range of 0.30 to 0.45, even if the calibration equation was not validated for these breeds!
CH4
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

11. Conventional Production traits Cheese properties Ketone bodies
It’s important to note that, given the limited number of data, the results have to be taken carefully … especially those for Normande breed where a high sampling error is expected with only 600 cows in production.
CH4
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

12. Conventional Production traits Cheese properties Ketone bodies
However, we can say/summarize that most MIR traits are moderately to highly heritable but most of them might not have obvious economic value (in Walloon Region of Belgium) for those dual-purpose breeds in conventional and even more in organic farming systems. Therefore, how can we use them ? Why not to predict lowly heritable traits or traits difficult to measure as for example longevity?
CH4
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

13. Prediction of longevity at early stages ?
production & novel MIR traits
Longevity, is by its association to animal robustness an important part of any breeding objective, also in dual-purpose cattle and even more in organic breeding systems.
However, information on longevity records can only be measured after an has done its productive life. Therefore, predictors of longevity traits could be very useful in order to breed for improved longevity at early stages.
It’s important to note that longevity is defined here in terms of number of lactations done by an animal!
EAAP 2018 Meeting Dubrovnik

14. Prediction of longevity at early stages ?
21,287 test-day records
2,988 primiparous dpBB cows
7,744 animals in pedigree
314 genotyped animals (108 ♀ and 206 ♂ )
EBV & GEBV for production & novel MIR traits
Using TD records from dpBB primaparous cows, EBV for conventional production traits and for some novel MIR traits were computed.
Similarly, GEBV were also computed from genomic information of about 300 genotyped animals.
EAAP 2018 Meeting Dubrovnik

15. Prediction of longevity at early stages ?
Different scenarios without and with genomics
Partial least squares analyses
(high correlated traits)
21,287 test-day records
2,988 primiparous dpBB cows
7,744 animals in pedigree
314 genotyped animals (108 ♀ and 206 ♂ )
EBV & GEBV for production & novel MIR traits
Different scenarios including or not genomic information were tested to predict longevity.
To this end, PLS analyses were performed in order to avoid major multicollinearity issues due to the fact some traits are highly correlated.
EAAP 2018 Meeting Dubrovnik

16. Longevity from MIR traits?
Scenarios
EBV (r)
GEBV (r)
S1: Milk, fat & protein yields
0.25
0.19
S2: Acetone, citrates & BHB
0.22
0.37
S3: S1 +S2
0.34
0.41
S4: S1 + UFA + SCFA + MCFA
0.42
0.29
S5: S2 + UFA + SCFA + MCFA
S6: S3 + UFA + SCFA + MCFA
0.51
0.47
The different scenarios were evaluated in terms of predictive ability of novel traits towards longevity,
The left column showing the results in terms of EBV, the right when using genomically enhanced EBV
Based on genotyped dpBB bulls with ≥ 10 daughters (N=160)
EAAP 2018 Meeting Dubrovnik

17. Longevity from MIR traits?
Scenarios
EBV (r)
GEBV (r)
S1: Milk, fat & protein yields
0.25
0.19
S2: Acetone, citrates & BHB
0.22
0.37
S3: S1 +S2
0.34
0.41
S4: S1 + UFA + SCFA + MCFA
0.42
0.29
S5: S2 + UFA + SCFA + MCFA
S6: S3 + UFA + SCFA + MCFA
0.51
0.47
Results were at the first glance surprising as the ability to predict was decreasing for traditional traits under genomics.
However different authors found that genomic correlation at the basis of this can also be different from results based on pedigree relationships.
Based on genotyped dpBB bulls with ≥ 10 daughters (N=160)
EAAP 2018 Meeting Dubrovnik

18. Longevity from MIR traits?
Scenarios
EBV (r)
GEBV (r)
S1: Milk, fat & protein yields
0.25
0.19
S2: Acetone, citrates & BHB
0.22
0.37
S3: S1 +S2
0.34
0.41
S4: S1 + UFA + SCFA + MCFA
0.42
0.29
S5: S2 + UFA + SCFA + MCFA
S6: S3 + UFA + SCFA + MCFA
0.51
0.47
Ketosis related traits showed promising results as did some major groups of fatty acids.
Based on genotyped dpBB bulls with ≥ 10 daughters (N=160)
EAAP 2018 Meeting Dubrovnik

19. Longevity from MIR traits?
Scenarios
EBV (r)
GEBV (r)
S1: Milk, fat & protein yields
0.25
0.19
S2: Acetone, citrates & BHB
0.22
0.37
S3: S1 +S2
0.34
0.41
S4: S1 + UFA + SCFA + MCFA
0.42
0.29
S5: S2 + UFA + SCFA + MCFA
S6: S3 + UFA + SCFA + MCFA
0.51
0.47
All scenarios behaved much worse in a GEBV setting when production traits were added.
Based on genotyped dpBB bulls with ≥ 10 daughters (N=160)
EAAP 2018 Meeting Dubrovnik

20. MIR traits ~ useful in 3 dual-purpose cattle breeds
Take home messages
Novel MIR predicted milk traits for dual-purpose cattle:
heritable  selection
promising early indicators of longevity (for dpBB)
Use of genomics:
Slight increase of reliabilities (not shown)
GEBV for novel MIR traits tend to be better predictors of longevity
In conclusion, the take home messages are:
MIR traits could be useful for dual purpose cattle breeds…
Indeed, MIR traits are heritable and then could be used for breeding and management purposes. They showed also promising results to predict longevity at early stages for dual purpose Belgian Blue breed.
Moreover, using genomic information, allow to increase slightly reliabilities and GEBV for MIR traits tend to be better predictors of longevity
MIR traits ~ useful in 3 dual-purpose cattle breeds
EAAP 2018 Meeting Dubrovnik

21. EAAP 2018 Meeting Dubrovnik
Acknowledgements
EAAP 2018 Meeting Dubrovnik

22. S. Vanderick1,2, F.G. Colinet1, A. Mineur1, R.R Mota1,
Genetic parameters of novel mid-infrared predicted milk traits in three dual-purpose cattle breeds
S. Vanderick1,2, F.G. Colinet1, A. Mineur1, R.R Mota1,
N. Gengler1, H. Hammami1
1 Gembloux Agro-Bio Tech, ULiège, B-5030 Gembloux, Belgium 2
EAAP 2018 Meeting Dubrovnik

23. Conventional Production traits Cheese properties Ketone bodies
In this slide, results for average daily h² over the lactation of each trait are summarized (means through the first-three lactations of these average daily h² for each trait) . Breeds are differentiated by colours and shapes of symbols.
Conventional Production traits
Cheese properties
Ketone bodies
Groups of FA
Minerals
Proteins
EAAP 2018 Meeting Dubrovnik

24. R² of calibration equation
min
max
Cheese properties
0.44
0.78
Groups of FA
0.77
0.99
Minerals
0.82
Proteins
0.69
Ketone bodies
0.62
0.89
CH4
0.70
EAAP 2018 Meeting Dubrovnik