Presented at the Twenty Sixth Ethiopian Society of Animal Production Annual Conference, Bahir Dar Ethiopia, 23-25 August 2018

1. The science of genomics and
livestock genetic improvement
Dirk Jan de Koning, Getinet Mekuriaw Tarekegn &
Erling Strandberg
Department of Animal Breeding and Genetics, SLU
Dj.de-koning@slu.se

2. Advances from breeding in the
devloped world
Species Trait 60s 2005 %-
increase
Broilers Days till 2 kg 100 40 60
Fillet, % 12 20 67
FCR 3,0 1,7 43
Layers Eggs/year 230 300 30
Eggs/ 1000 kg feed 5000 9000 80
Source: Table 1 i Van der Steen et al. J. Anim. Sci. 2005. 83:E1-E8
woodleywonderworks under Creative Commons

3. Thanks to plant and animal
breeding
60s 2005 Reduced
acreage
Feed(kg) Ha Feed
(kg)
Ha
1000 kg lean
pork
11750 6,5 5880 2,6 2,5x
1000 kg broiler
meat
3000 1,7 1700 0,37 4,6x
10000 eggs 2000 1,1 1111 0,24 4,6x
Creative Commons: Neil Palmer Creative Commons: woodleywonderworks Creative Commons: jere-me/

4. The observed trait is sum of many genes
and environmental factors
Complex Traits

5. Classical model
Genotype
environment
Phenotype

6. Genomics Era Model
Phenotype
Environment
QTL
QTL
QTL
QTL
QTL
QTL
Genotype

7. Marker Assisted Selection
Accelerate genetic progress
Measure DNA Markers early in life
Even in embryos
Sex limited traits
Milk
Litter size
Traits measured in relatives
Meat quality traits!

8. Three starting points for MAS
Ease of
Detection Use
Functional mutations
- known genes
Q
q
M
m
Q
q
Markers in pop.-wide LD
with functional mutation
Markers in pop.-wide LE
with functional mutation
Q
q
M
m
genes
GAS
LD-markers
LD-MAS
LE-markers
LE-MAS

9. Genomic Selection
Phenotype
Environment
Q
T
L
Q
T
L
Q
T
L
Q
T
L
Q
T
L
Q
TL
Q
T
L
Q
TL
Q
TL
Q
T
L
Q
T
L
Q
T
L
Q
T
L
Q
T
L
Q
T
L
QTL
QTL
QTL
QTL
QTL
Whole genome
SNP genotypes
A better Black box

10. Genomic Selection

11. MAS
• Find QTL or genes and
select specifically for
favourable alleles
• Need strategy to
combine with EBV
• LE-MAS computationally
intensive
• LE-MAS has major
genotyping requirements
Genomic Selection
• Estimate effects
across all markers
and select on the
sum of effects
• Replaces EBV
• Can be very
computationally
intensive
• Major genotyping
requirements

12. Genomic Selection: Accuracy
Very important when considering Genomic
Selection:
What accuracy can I achieve?
How many animals do I need for training?
How many markers do I need?
What is the cost-benefit ratio?

13. Genomic Selection: A little
example

14. Livestock state of play

16. Generation intervals reduced dramatically
Sires for bulls: ~7 => 2,5 years
Dams for bulls: 4 => 2,5 years
Selection differentials quite constant
Genetic trends improved a lot
Genetic gains increased
50-100% for yield traits
3x – 4x for traits with low heritability

19. International efforts for tricky
traits
Some traits are very expensive or difficult to measure. For
example methane emission and individual feed intake.
Large collaborations: each country (including Sweden)
measures a number of cows
Concern: genetic differences and GxE

20. Genomic Selection
• Has doubled genetic progress for yield traits in dairy, 2-4-
fold improvement for health traits!
• Other species following suit.
• Special case for crossbreeding species.
• Crop breeding has been turned on its head by genomic
selection
• How do we deliver the benefits of modern breeding to
low-income countries?
• Faster in crops because seeds are easily stored and distributed!

21. Options for genomic selection in
low income countries
• Nucleus breeding programs
• Centrally organized
• Generic breeding goal
• Good potential for species like poultry
• Community based breeding programs
• Locally organized
• Use locally adapted genetic resources
• May struggle to get suitable reference population
• Any participatory approach needs immediate benefits for
the participating farmers: not in the future.

22. Current examples
• African Dairy Genetics Gains
• Funded by ‘GATES’ foundation
• Strong stakeholder involvement
• Farmers submit data to the ADGG platform
• Farmers receive feedback via iCOW:
=> 3 SMS/week
 Drip feeding manuals to farmers
 Mainly improved farm health
• IlRI’s Livestock Genetics program: LiveGene

24. Useful links
Misperceptions about livestock:
https://www.slideshare.net/ILRI/extinction-livestock-
smithoct17
TED talk on ADGG:
https://africadgg.wordpress.com/2018/02/09/livestock-
genetics-program-works-with-farmers-to-boost-nutrition-in-
africa/
B3 Africa:
http://www.b3africa.org/