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