1. J.R. Thomasen, H. Liu and A.C. Sørensen
Pedigree inbreeding is not a good estimator of true inbreeding in genomic dairy cattle breeding schemes
J.R. Thomasen, H. Liu and A.C. Sørensen
EAAP, Tallinn, Estonia

2. Hypothesis
Pedigree inbreeding underestimates the true inbreeding in genomic breeding schemes
Reasoning
Neutral locus assumption is violated in all breeding schemes
and in genomic breeding schemes in particular
True inbreeding of an individual: The proportion of homozygous IBD markers

3. Scenarios Large High LD Holstein Small Jersey Low LD Red Reference
Population Size
Population
Structure
Mimicking
the breeds
Large
High LD
Holstein
Small
Jersey
Low LD
Red

4. Stochastic simulation design
Founder population
Sire reference population
Proven bull schemes
Genomic Breeding Scheme
3000 generations
20 years
10 years

5. Simulation of LD structure
Founder population
Sire reference population
Proven bull schemes
Genomic Breeding Schemes
3000 generations
20 years
10 years

6. Selection and Evaluation
Truncation selection
Total merit Index
2000 QTL’s
Single Step GBLUP
Evaluation
Genetic gain – ΔG (€/year)
Pedigree inbreeding - ΔF-PED (%/generation)
True Inbreeding - ΔF-TRUE (%/generation)

7. Proven bull schemes Large reference population
10,000 bulls in reference over 20 years
500 young bulls tested yearly
20 proven bulls selected yearly
Small reference population
1,000 bulls in reference over 20 years
50 young bulls tested yearly
5 proven bulls selected yearly

8. Genomic breeding scheme
Breeding nucleous
10,000 cows
2000 genotyped bull calves
100 young bulls
2000 genotyped heifers
(10 progeny)
200 donors
(Reference)
(Reference)

9. Development of inbreeding
Proven bulls scheme
Genomic scheme

10. Inbreeding in proven bull schemes
(€/yr)
ΔF-PED (%/gen)
ΔF-TRUE
(%/gen)
Relative
Underest.
Large
21.8
0.66
0.69 4%
Small
20.4
2.27
2.36

11. Inbreeding in genomic schemes
Reference LD ΔG
(€/yr)
ΔF-PED
(%/gen)
ΔF-TRUE
Relative
Underest.
Large
High
42.0
0.23
0.44
50%
Small
35.6
0.42
0.99
58%
Low
38.5
0.29
0.46
37%

12. Inbreeding in genomic schemes Small reference population
Sires
Donors
Geno.
heifers/yr ΔG
(€/yr)
ΔF-PED
(%/gen)
ΔF-TRUE (%/gen)
Relative
Underest.
100
200
2000
35.6
0.42
0.99
58% 50
34.9
0.45
1.03
56%
4000
37.4
0.32
0.89
64%

13. Take home messages
Pedigree inbreeding underestimate true inbreeding in genomic schemes
Inbreeding is lower in genomic schemes using many young bulls than in progeny testing schemes
Unbiased estimator for rate of inbreeding needs genomic information