Dairy Genomics Program of
the Centre for Tropical
Livestock Genetics and Health
Tropical Dairy Genomics
Karen Marshall, ILRI
CTLGH/BMGF/DFID Meeting, Nairobi,
17-19 May 2017

CTLGH-BMGF-DFID results framework (bold=resourced)
Outputs Existing projects Proposed projects *CN submitted
1.1.1 Define and
characterize cattle
adaptability or
productivity traits
Dairy cattle adaptation - feed (drought
tolerance)*
Dairy cattle adaptation - disease*
1.1.2 Identify putative
causal variants linked to
cattle
adaptability/resilience or
productivity traits
Signatures of selection for adaptation e.g.
heat
Genomic variants for milk and other ADGG
traits
1.1.3 In collaboration
with ADGG develop
genomic tools and/or
prediction algorithms to
aid the selection of
superior dairy cattle
Genomics Reference Resource for African
Cattle
SNP-chips for (a) African cattle genome
interrogation, (b) breed composition of
African cattle
Genomic tools for genetic improvement of
smallholder dairy cattle*
Suitability index for screening global dairy
cattle for use in East Africa*
1.1.4 Identify cattle
adaptability or
productivity genetic/
metagenomic variants
for use as proof of
Literature study /
new variants arising from program studies
in later years
With ADGG
With CTLGH P3 (reproductive
technologies & gene editing)
With CTLGH P4 (health genetics)
and ADGG
With ADGG
With ADGG
With African partners & CTLGH P3 (gene
editing) and P4 (health genetics)
(a) With CLTGH P4 (health genetics)
Lead
person
KM
EW
JH
JG
KM
??
??

Background
 We need to breed animals fit for a future changed environment
 In tropical livestock systems, we do not have sufficient knowledge on
adaptive capacity of different livestock genotypes, or mechanism
underpinning adaptation, to do this
Direct and indirect impacts of climate change on livestock systems
Thornton PK, Boone RB, Ramirez-Villegas J. 2015. Climate
Change Impact on Livestock. CCAFS Working Paper No. 120.
(1) Dairy cattle adaptation to protracted nutritional deficits

Proposal
 To initiate studies on adaptation of dairy cattle breeds / cross-breeds in East
Africa, including the indigenous breeds and recently popularizing cross-breeds
 Focus traits –
 the sensitivity of milk production to feeding levels
 ability to recover milk production after protracted nutritional deficits
(such as that observed during seasonal dry spells, droughts)
(1) Dairy cattle adaptation to protracted nutritional deficits
Why these traits?
feed is a key determinant of dairy
production in East Africa
seasonal changes in feed quantity
and quality are large
feed variability is likely to increase
with increased climate variability

Key deliverables
 Renovated livestock research facilities on ILRI’s
farm, facilitating assessments of dairy cattle
productivity under different environmental
conditions (including feed levels)
 Understanding of the effect of East African
dairy cattle breed / cross-bred type on the:
 sensitivity of milk production to feeding level
and quality
 and animals’ ability to recover milk production
after periods of protracted nutritional deficit
(1) Dairy cattle adaptation to protracted nutritional deficits
G x E interaction
The interaction of genotype
and environment that
produces the phenotype

(2) Genomic tools for genetic improvement of smallholder dairy cattle
Background
 The Africa Dairy Genetic Gains (ADGG) project
is a pilot project working in Ethiopia and
Tanzania that is exploring the methods and
structures that will support sustainable
genetic improvement in East African
smallholder dairy cattle populations
 Interest in testing a reduced SNP assay to
determine the breed composition of East
African cross-breed dairy cattle, for
applications such as:
 certification of breed composition of crossbred
bulls for natural mating or AI;
 farmer knowledge of cow breed composition –
at time of purchase, or to inform selection of
appropriate bull breed-types

ILRI farm renovations
Feed measurement facilities (12
units)
Automated milking machines (4) and
accessories
Automatic weight-scale
Weather station
Feed preparation equipment – feed
mixer, chaff cutter
Milk analyser (fat & protein)
Computer + back-up
(2) Proposed livestock research facilitites
ILRI’s Kapiti station: 32,000 acres in semi-arid environment,
currently running 2200 cattle and 1600 small ruminants

(2) Genomic tools for genetic improvement of smallholder dairy cattle
Proposal, key deliverables
 Determine whether the reduced snp assays for exotic dairy proportion & parentage assignment, developed
in DGEA and ADGG, can be used in other dairy cattle populations outside East Africa.
 via combining data from Ethiopia and Tanzania (ADGG) with data from Senegal and Malawi
 Deliverable = reduced SNP set(s) for determining breed composition (as exotic dairy proportion) and
parentage assignment for use in African crossbred dairy populations
 Determine whether it is possible to impute from low density assays to high density of snp with sufficient
accuracy to provide useful accuracy of EBV in crossbred dairy populations outside of East Africa.
 via combining data from Ethiopia and Tanzania (ADGG) with data from Senegal and Malawi
 Deliverable = reduced snp set that will allow imputation to sufficient number of snp to construct accurate
relationship matrices for use in African crossbred dairy populations
 Determine the accuracy of European and/or indigenous breed composition to be estimated from snp data.
 i.e. extending form proportion indigenous versus exotic to actual breed-type
 using data from a large farm with a variety of crosses, and pedigree and performance records: this will be
combined with ADGG data for refined breed recommendations
 Deliverable = reduced snp set that estimate individual breed proportions with sufficient accuracy for use
in the ADGG genetic improvement program; improved estimates of performance of crosses to different
dairy breeds, and resulting recommendations for use.

(3) Suitability index for screening the global Holstein population
Background
 The ranking of dairy sires is likely to differ between high input dairy systems
in developed countries and the lower-input dairy systems in Africa (G x E)
 Currently we do not have a tool for screening the global Holstein – or other
dairy breed - populations for their suitability as parents of crossbred animals
in Africa
.
A holstein-friesian bull at the Kenya Animal Genetic
Research Centre. Credit, P. Karaimu, ILRI.
 Such a tool can be developed using an
approach called Reciprocal Recurrent
Genomic Selection (RRGS)
 RRGS involves using information
collected on crossbred animals within a
commercial environment to drive
selection decisions in the purebred
nucleus animals from which they derive.

Proposal, key deliverables
 Using genotype data from ADGG (5000 – 10,000
crossbreeds) and from pure Holsteins, develop
and validate a genomic prediction equation for
a “suitability index” based on the RRGS model
 For a index of traits (aligning to ADGG breeding
objective)
 Deliverable = Validated genomic prediction
equation for a “suitability index”
 Screen genotyped Holstein bulls (potentially
from Genus ABS) using the suitability index
 Deliverable = identified Holstein bulls suitable for
use as parents of crossbred animals in East Africa
– this information shared with industry partners
(3) Suitability index for screening the global Holstein population

The Centre for Tropical Livestock Genetics and Health (CTLGH) is a joint venture
between the International Livestock Research Institute, the University of
Edinburgh, & Scotland’s Rural College, currently funded by the Bill and Melinda
Gates Foundation and the CGIAR Livestock and Fish CRP.
Karen Marshall, the International Livestock Research
Institute, kmarshall@cgiar.org