Drawing from the indigenous african livestock genomes a dart aimed at sustainability
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Transcript of Drawing from the indigenous african livestock genomes a dart aimed at sustainability
Drawing from the indigenous African livestock genomes
- a dart aimed at sustainability
Dr. Mary Ndila Mbole-Kariuki
”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
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
Effects on the genetic resources
� Loss of genetic diversity
� Loss of adaptive traits
� Endangered
Why has sustainability continued to be evasive in Africa?
Needle in haystack
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
Study site
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
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
Genetic characterizationPopulation structure
PCA analysis
65% variation
14
%
vari
ati
on
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
Key: proportion of calves with “SUBSTANTIAL”
European introgression per sub location
Legend: Average proportion of
European taurine introgression per
sub locations
Key: proportion of calves with “MODERATE”
European introgression per sub location.
North to south genetic cline
Legend: Average proportion of
European taurine introgression per
sub locations
r = 0.82 P < 0.0001
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
Key: proportion of calves with “MODERATE”
European introgression per sub location.
Selection against
North to south genetic cline
Legend: Average proportion of
European taurine introgression per
sub locations
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
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
1
2
3
6
4
5
7
EAST AFRICAN SHORTHORN ZEBU
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
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?
Ecologically important traits
Economically important traits
Strike a balance – 3 E’s
� Exotic * Indigenous?
� Indigenous * Indigenous?
Environment
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
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
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
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
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
DISCLAIMER
Acknowledgements
� Prof. Olivier Hanotte (UoN)
� Dr. Miika Tapio (MTT)
� Dr. Tad Sonstegard (USDA)
� Farmers
� Wellcome Trust
� IDEAL fraternity
THANK YOUTHANK YOUTHANK YOUTHANK YOU