Sustainability
Farmers – sustainable populations uphold Darwinian adaptations in indigenous breeds
Scientists – sustainable use of Africa’s genetic resources landscape genomics, genomic selection
Breed improvement programs – sustainable productivity match projects to environments
Governments/policy makers (AU-IBAR) – policies driving sustainability – CAIS stock indigenous breeds genetic material, sharing genetic material across borders

1. Drawing from the indigenous African livestock genomes
- a dart aimed at sustainability
Dr. Mary Ndila Mbole-Kariuki

2. ”It’s been proven that of all the interventions to reduce
poverty, improving agricultural productivity is the best. All
the other different economic activity — yes it trickles down.
But nothing as efficiently as in ” – Bill Gates
(2013)
Small-holder farmers
Over 500 million small-holder farmers
~2 billion depend on it for livelihoods
Produces 80% of food consumed in Asia, sub-
Saharan Africa

3. Challenges livestock production faces in
Africa – small holder farmers
“Negative selection”
Prevalence of disease and disease vectors
Continual ineffective traditional animal husbandry
practices
Evident knowledge gap - BIP
Poor extension services
Eminent climate change

4. Effects on the genetic resources
Loss of genetic diversity
Loss of adaptive traits
Endangered

5. Why has sustainability continued to be
evasive in Africa?
Needle in haystack

6. In 2009 …..
Indigenous East African Shorthorn Zebu (EASZ) – Western Kenya
An Admixed population – indicine and taurine
Well adapted to aridity and heat
Resistant/tolerant to infectious diseases (ECF) and vectors (Ticks)
Embarked on,
Characterizing on a genome level the population structure of
EASZ
Identifying imprints of genetic selection through phenotype-
genotype associations for disease and non-disease traits

7. Study site

8. Study design
Recruitment flow chain
552 (3-7 days old) calves and followed-up for 1 year period
Calves were exposed to natural disease and vector challenges
No veterinary intervention was administered apart from
euthanasia of critically ill animals
Routine rural farm practices
Chiefs
AHA
Farmers

9. Genotypic data
Illumina® BovineSNP50
Mapped against University of Maryland genome 3.1 assembly
Number of SNPs
Mapped autosomal SNPs 54436 (96%)
Unmapped autosomal SNPs 1066
Unknown chromosomes 104
Sex chromosome 1341
Total SNPs 56947

10. Genetic characterization
Population structure

11. PCA analysis
65% variation
14%variation

12. Evidence of European taurine introgression
CATEGORY 1 CATEGORY 2 CATEGORY 3
Pure from
European
introgression
(x≤1.56%)
6 or more
generation
Moderate
European
introgression
(1.56%>x<12.
5%)
4-5 ET
generation
Substantial
European
introgression
(x≥12.5%)
2-3 ET
generations
N=425 N=94 N=29

13. Key: proportion of calves with“SUBSTANTIAL”
European introgressionper sub location
Legend: Average proportion of
European taurine introgression per
sub locations

15. Key: proportionof calves with“MODERATE”
European introgressionper sub location.
Northtosouthgeneticcline
Legend: Average proportion of
European taurine introgression per
sub locations
r = 0.82 P < 0.0001

16. Breed Improvement programmes
Rural Development Project (1979-1989)- Kitinda
dairy Bungoma
Kenya – Finland Livestock Development
Programme (1991-2003)
Services offered:
AI upon request, in-calf heifers, bull schemes
Breeds used: Holstein, Aryshire, Jersey, Guernsey
Impacts
Offspring boom Bull schemes 84,749

17. Key: proportionof calves with“MODERATE”
European introgressionper sub location.
Selection against
Northtosouthgeneticcline
Legend: Average proportion of
European taurine introgression per
sub locations

18. Present Western Kenya EASZ genetic state
Economically
important traitsEcologically
important traits
This shift of focus is to a perceived
economically beneficial animal as
opposed to an ecologically fit one

19. Impact on the indigenous EASZ genome
integrity
All calves (n =
548)
Moderate and
substantial calves (n
= 123)
Non-
introgressed
calves (n = 425)
Between
calves
ET < 2.2e-16 *** <2e-16 *** -
AT 1 1 1
AZ <2e-16 *** < 2e-16 *** 1

20. 1
2
3
6
4
5
7
EAST AFRICAN SHORTHORN ZEBU

21. R2 value Correlation
coefficient
P value
Easz AT /sheko AT 0.7869 0.887 6.668e-11
R² = 0.7869
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0.5
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35
shekoAT
Linear (shekoAT)
chr x

22. Case studies
Farm – Africa dairy goat
project - Ojango et al.
2010a
Kenya Dual Purpose Goat
Development project
(KDPG) Ojango et al. 2010b
Dairy Goat development
programme (DGDP) –
Ayalew 2010
Establishment of synthetic
populations?
Lack of continual financial
and extension services
support?
Beneficial genotypes in
wrong environment?

23. Ecologically
important traits
Economically
important traits
Strike a balance – 3 E’s
Exotic * Indigenous?
Indigenous * Indigenous?
Environment

24. Calls for Conservation - utilisation
Effective population size – important genetic measure and
fundamental in understanding conservation.
Reflects effects of drift or inbreeding
Characterizes the population diversity
Highlight events that shape a population
Used a marker-based approach using linkage disequilibrium
E(r2)=[1/(1+4Nec)]+(1/n)
Indicator of genetic decline – small Ne predicates low genetic diversity
unsuitable for population survival

25. Fst statistics Autosomes P value
Fst (subpopulations/total) 0.0033 0.09
Fit (Individual/total) 0.0217 0.07
Fis
(Individual/subpopulations)
0.0185 0.03
Fst statistics

26. Stop the genetic diversity melt-down and seek out
the adaptive traits before they are entirely lost and
make them work to the farmers’ advantage
For if one link in nature’s chain might
be lost, another might be lost until
the whole of things will vanish
piecemeal – T. Jefferson

27. Sustainability
Farmers – sustainable populations uphold Darwinian
adaptations in indigenous breeds
Scientists – sustainable use of Africa’s genetic resources
landscape genomics, genomic selection
Breed improvement programs – sustainable productivity
match projects to environments
Governments/policy makers (AU-IBAR) – policies driving
sustainability – CAIS stock indigenous breeds genetic material,
sharing genetic material across borders

29. Success stories
Carora-Holstein crosses - Carora (composite venezuelan
breed) - slick hair gene and exotic Holstein
Girlando – Gir (zebu breed in Brazil) and exotic Holstein
Kurolier chicken (indigenous and exotic crosses)
Kenya Dual purpose goat – crosses of indigenous East
African and Galla with exotic Toggenburg and Anglo-
Nubian

30. DISCLAIMER

31. Acknowledgements
Prof. Olivier Hanotte (UoN)
Dr. Miika Tapio (MTT)
Dr. Tad Sonstegard (USDA)
Farmers
Wellcome Trust
IDEAL fraternity

32. THANK YOUTHANK YOUTHANK YOUTHANK YOU