ILRI program outline: Livestock
Genetics
Okeyo Mwai, Steve Kemp and Karen Marshall
ILRI Institute Planning Meeting
4-7 October 2016

Vision
Photo: www.impatientoptimist.com
Livestock Genetics program is a valued and globally
recognized partner which provides:
• state-of the-art breeding technology and data platforms
• leadership in the areas of gene discovery, genetic diversity
characterization utilization of the results in integrating these
in the R&D contexts to continuously improve, deliver and
promote use of more productive and healthy livestock under
tropical systems
The desired program outcome:
Appropriate livestock breeds are readily available, affordable
and widely used by poor women and men livestock keepers,
resulting in increased livestock productivity, improved food and
nutritional security, better livelihoods and improved natural
resource that support them.

Objectives
• To determine the most appropriate genetic
improvement strategy for different systems
• Discover genes responsible for productivity &
resilience and develop/adapt technologies to efficiently
incorporate them in breeding programs
• Design and support implementation of sound breeding
programs & delivery of the desired genetics to a range
of livestock keepers
• Identify policy gaps & provide evidence for and need
for policies and institutional arrangements that would
enable improved access, sustainable use of livestock
genetic resources.

Why genetics: Need to close the livestock productivity
gap
0
5
10
15
20
25
30
35
40
0 1 2 3 4 5 6 7 8 9 10
Kgofmilkperday
Months in Milk
Figure 1: Realized lactation curves of improved (crossbred or higher) dairy cows achieved by
different farmer types in Kenya
Commercial/Intensive dairy farmers –
~6,500 kg/lactation --- ~2% of farmers
Best smallholder farmers - ~2,500
kg/lactation --- ~5% of farmers
Average smallholder farmers --- ~1,400
kg/lactation --- >90% of farmers
• Mitigate risks (e.g. effects of CC,
emerging diseases (zoonotics))
• Work towards ensuring equity (focus
on chicken, and small ruminants and
crossbred dairy cattle & buffalos to
widen our reach)
• Ensure environmental health (e.g.
increasing productivity/animal to
reduce GHG emissions)

Assessment
tools
Improved
breeds of
livestock
Multiplication
& delivery
systems
Policy
guidelines
Consideration of a
future changed
environment
Implementation of
delivery systems by
stakeholders
Genetic improvement strategy and
delivery system designed with
stakeholders
Policy guidelines
adopted by
stakeholders
Women and men
resource poor farmers
sustainably utilising
improved livestock
genetics
Access to
inputs
including
animal health-
care and feed
Implementation of
genetic improvement
strategy by
stakeholders
Gender focus
Consideration
of gender and
youth issues
= Identified sets of assumptions
Sub-idos
Stakeholde
r capacity;
enabling
environme
nt
Stakeholde
r capacity;
enabling
environme
nt
Stakeholde
r capacity;
enabling
environme
nt
Stakeholde
r capacity;
enabling
environme
nt
Stakeholders = policy makers, national research and
development partners, investors, the private sector,
women and men livestock keepers
Access to
markets
Theory of change

Program Strategy
Short term:
• Apply existing ICT & Genomic technologies to better understand the existing genetic diversity
• Roll out systems for on-farm testing and models for delivery of promising existing genetics
Medium term:
• Identification of genes / gene-networks underpinning important traits and incorporate these in the
breeding programs
Long term: Integrate breeding and molecular technologies to design and deliver optimized genetcs
programs

What do we work on:
Sheep
Dairy cattle
Pigs
Dual purpose
cattle
Poultry Goats

Where we work
Future livestock demand scenarios indicate that most of the supply of livestock products is likely to come from
smallholder and agro/pastoral production systems for the foreseeable future in Africa (Herrero et al., 2014) and Asia
(Hemme et al., 2015). Therefore, the Livestock Genetics Program will target the smallholder sector for achieving
sustainable impact at scale.
Eastern Africa
(chicken, dairy
cattle, pigs,
sheep & goats
India &
Pakistan(cattle,
goats
West Africa
(Nigeria &Burkina
Faso)Chicken,
sheep and goats
Central America
Nicaragua (dual
purpose cattle)
China (all key
species)
Roslin, UK (cattle, chicken
and pathogens)

Existing Facilities
Location Facility
ILRI Nairobi
Joint ILRI-BecA laboraorites in Nairobi,
Kenya
Reproductive platform in Nairobi, Kenya
Biobank in Nairobi, Kenya
Farm – ILRI farm and “Kapiti” research
station in Kenya
Beijing, China Joint CAAS/ILRI laboratory in Beijing, China
ILRI Addis Ababa Molecular lab
Other Partners
Roslin Institute and NARS
Centers
Experimental flock at Debre Berhan,
Tanzania and Nigeria
Reproduction and Genomics labs at Roslin,
UK

On-going work:
• Most of on-going and planned projects span across our 4 research themes
• The activities have integrated capacity development elements
• Include collaboration with other ILRI Programs
• Implemented/to be implemented in close collaboration with our core strategic
ARIs, RRO, NARES and Development and Private sector partners
Integration
synergy

Assessments of animal genetic resources (AnGR) and use
$ ‘big data
capacity’
Biorepository:
~500,000 samples
Phenomic and genomic
assessment of AnGRs:
-Breed comparison, environmental
effect
-Identification of genes / gene-
networks underpinning important traits

What are the most appropriate genetics improvement
strategies?
We consider:
• Stakeholder needs and
preferences
• Present and predicted
future production
system
• Sustainability
mechanisms
• Required scale to
achieve impact
What is the most
appropriate genetic
improvement
strategy?

Reproductive
technology
platform – gene
editing
Improved breeds of livestock
Introduction or
creation of
improved breeds
of livestock – with
national partners
Recording and
feedback
platform
Analytical platforms –
combining genetic and
phenotypic information to
identify elite breeding animals
Breed
substitution
Cross-breeding
New breed-types (gene-editing)
Within breed improvement

ACGG- “More productive chickens for African
smallholders”
Identity
Appropriate
Chicken
Technology
Test
Technology
On-Station
and On-Farm
Select Farmer
Preferred and
High
Producing
Strains
Support Private
Sector in the
Implementatio
n of a Long
Term Genetic
Gains Program
PPP
Development
for the
Multiplication
of Select
Technologies
Impact
Increased
Smallholder
Productivity
in SSA

ACGG- Long Term Genetic Gains
National
Agricultural
Research System
(NARS)
The platform members
(ILRI, CTLGH, WU, NARS
etc)
Private sector
breeding
companies (e.g
Silverlands,
TZ/Amobeye,
NG
ILRI –Overall
Coordinatio
n
Vision
Annual 2% Genetic
Gains
Objective
Sustainable Genetic
Gains Program in
Sub-Saharan Africa
Maintained
By the Private
Sector

(1) Data analytics system
(DPRC)
Farmer/Herd
Bench marking
and decisions Optimize Realized
Productivity for
farmers
P
r
o
d
u
c
ti
v
it
y
Time
(3) Digital
Information
Capture and
farmer feedback
& actors
interaction
Systems
(2)
improved/certifi
ed bulls/heifers
ADGG- More productive and resilient cows for smallholder
systems

Survived Died
%
Survived
Fisher's
Exact p
Trial 1
Progeny of
ZI3167 3 0 100
Control 0 9 0 0.0045
Trial 2
Progeny of
ZI3167 4 6 40
Control 1 11 9 0.14
Trial 3
Progeny of
ZI3167 12 3 80
Control 0 8 0 3.4x10-4
Combined Progeny of 3167 19 9 68
Combined p
(Stouffer's
method)
Control 1 28 4 2.11x10-5
T. parva Tolerance

• Complete analysis of whole genome sequences of all 33
phenotyped progeny
• Study effect of different endpoint variables on analysis
• Phenotype further offspring of 3167 including F2
generation to refine study – sequence and add to analysis
• Identify further putative tolerant families
ILRI
Phil Toye, Annie Cook, Tatjana Sitt, Gideon Ndambuki
Roslin
James Prendergast, Ivan Morrison, Tim Connelley
Immediate Plans

Multiplication and delivery systems
Nucleus
Multiplier
Commercial
Adaptation of
reproductive
technologies to
the local
situation
Establishment
of business
models for
delivery
(e.g. PPP)

Cross program linkages- Greater impact through
partnerships within and outside ILRI
Significant interaction between other
programs at value chain levels:
Focus on joint project design, technology
development/testing and delivery, influencing:
 Sustainable Livestock production systems-Livestock
AVCD
 Policy, Gender –Dairy- AVCD,ADGG.ACGG
 Forage and Feed Resources- gene discovery/
genomics for improvement, Genetic Gain
 Human and Animal Health- pathogen/host resistance,
Microbiome research (chicken & dairy)
 Impact at scale-AVCD, ADGG/links with development
partners
 Tool & Data systems support- RMG, Big data.
Significant yield gaps are seen on-farm. While dramatic increases in yields have historically been driven by highly
accelerated genetic gains, the full potential is not realized without the delivery of appropriate technologies,
improve feed, disease management, and delivery.
- Environment
- Climate
- Health
- Feeding
- Water
-inputs & Market Access
Genotype
Home
consumption,
Aggregation,
Processing, Sale
Husbandry,
Knowledge
Exchange
Home
consumption,
Aggregation,
Processing, Sale
Husbandry,
Knowledge
generation &
Exchange
Productivity
Growth

Support services- What we need to enhance efficiency
and increase our impact
• Better reporting systems that meet
institutional and donor/CRP needs
• Legal expertise in data, ABS -
becoming increasingly important as we
partner more with the private sector
New Support Services
• More proactive engagement and crisis
management/ passive type of actionsResearch Compliance
• Aggregation and maintenance of data
• Standardized protocols and support
around metadata, collection, and
sharing
Data Systems
• Relationship management to
strengthen and develop partner
linkages
• Support in engaging private sector
partners
Partnership
Development
• Inclusive engagement with Cap Dev
& BDU to enable adequate
resourcing and frameworks for more
effective staff/internships with our key
partners
• Business development/resource
mobilization support
• Tailored Cap Dev tools, trainings, and
deliverables
Internships/staff
exchanges Adequate/Stable Funds +
Increased Capacity
Timely
engagement/implementa
tion of compliance issues
Additional expertise to
manage a world Class Data
Infrastructure + Large Open
Access Datasets
Stronger BDU to better
support partnerships +
PPPs
Better/more responsive
systems & legal expertise
in ABS related issues

New scientific and resource mobilization opportunities-
What’s next?
New Scientific/Investment Opportunity Potential
Partner/Donor
Phenomics platforms and innovative applications of ITC for crowdsourcing of
data
BBSRC with SRUC/CTLGH,
Google Foundation
Dairy systems in West Africa
Pig systems in Africa and Asia
Buffalos in Asia & Africa?
Camels in Africa
Local & International
Foundations and specific
Countries
Comparative Genomics:
• Innovative applications of genomics to study host/pathogen genomes
and relate to development of new Genotypes (genome editing),
medicines/vaccines)
• Development of affordable multi purpose genomic chips for breed
composition determination and support genomic selection
SRUC/CTLGH-BBSRC
New assisted reproductive technologies: Links with genomic/transgenic
research
• Communication
• PPP models to develop/manage biorespository/bio-banks with geo-
referenced materials that are linked to genome sequences, gene
expressions phenotypes
BBSRC
Partnerships with ARIs, genomic databases and Development agencies to
access digital genetics resources and finances to respectively undertake
blue sky genomic data-mining research and deliver development
outcomes and impacts
Various Foundations

Time for a new search for variation underlying tropical adaptation and
productivity
Identify and make use of the genetics
underlying natural variation.
There has been no systematic search for
the genomic basis of adaptation. Because
until now we have had no validation
tools and no delivery tools.
New Genome Editing tools change the
landscape.

Identify and deliver variants associated with adaptation
Genotyping Phenotyping
Adapted &
productive
livestock
Genome editingTargeting
Data systems
Delivery systems

Applied research application of genetics
Senegal Dairy Genetics
What is the most appropriate cattle breed-type
for the production system & environment?
Via trade-off analysis – productivity, livelihood
benefit, environmental sustainability, food safety
 3500 animals from 220 households monitored for almost
2 years- production, economic, gender data
 Different breeds / cross-breeds & management levels
 Breed-types assigned based on genomic data -
~30% match between farmer assigned breed-type & that
from the genomic data

Herd size of 8 cows; non-transhumant
0
100,000
200,000
300,000
400,000
500,000
IndigenousZebu
IndigenousZebu
IndigenousZebuby
Guzerat
IndigenousZebuby
Guzerat
IndigenousZebuby
BosTaurus
IndigenousZebuby
BosTaurus
HighBosTaurus
* ** * ** ** *** ****
Householdprofit(CFApercowper
annum)
Breed type and management level
8.0 fold difference
2.4 fold difference
Applied research application of genetics

Asked similar research questions -
results influenced a donor to
further invest in systems for dairy
cattle genetic improvement and
delivery systems in East Africa
Private-public partnership for
Artificial Insemination Delivery
(PAID)— led by Land O’Lakes
International
African Dairy Genetics Gains
(ADGG)
Dairy Genetics East Africa
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dailymilkyield(l/day)
Herd environment level
21-35% 36-60%
Applied research application of genetics

This presentation is licensed for use under the Creative Commons Attribution 4.0 International Licence.
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ILRI thanks all donors and organizations who globally supported its work through their contributions to the CGIAR system