CTLGH tropical dairy
genomics programme
Karen Marshall, ILRI
BMGF Learning Visit, Edinburgh
15 March 2018

Major yield gaps need addressing
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1600
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100,000
200,000
300,000
400,000
500,000
600,000
Indigenous
Zebu
Indigenous
Zebu
Indigenous
Zebu by
Guzerat
Indigenous
Zebu by
Guzerat
Indigenous
Zebu by
Bos Taurus
Indigenous
Zebu by
Bos Taurus
High Bos
Taurus
* ** * ** ** *** ****
Household profit (CFA per cow per annum) Milk yield (liters per annum)
Breed
Management
level
Improved breeds &
management 
8 x household profit;
7.5 x milk yield
Senegal study
Packaged interventions, including on genetically improved animals, can reduce yield gaps

Vision of the tropical dairy genomics program
The program aims to
facilitate the application of genomics to
dairy production in the tropics
for: increased livestock productivity,
enhanced livelihoods of the rural poor,
increased food and nutritional security,
a more sustainable environment.
Working closely
with partners,
particularly
implementers of
genetic
improvement
programs
Addressing
constraints to
genetic
improvement
programs that can
be solved by
genomics
Both shorter and
longer-term vision

Scientific portfolio – 3 main focal areas
Support to
African dairy
cattle genetic
improvement
programs
African cattle
functional
genomics
Understanding
African cattle
adaptation

Support to genetic improvement programs
Means by which the
technical solutions
will result in
outcomes and impact
(=key to the programs
TOC)

Support to genetic improvement programs
Means by which the
technical solutions
will result in
outcomes and impact
(=key to the programs
TOC)
Increased rates of
genetic gain
Increased value of ADGG
model and allow scale-out to
other populations

African cattle functional genomics
The origin and subsequent evolution of African cattle breeds 
much greater genetic diversity between breeds in Africa than for any other continent 
unique natural resource for gene detection
Resources
• ADGG: genome wide association studies
• Genomic Reference Resource: signatures of selection
Putative
functional
mutations
• Range of approaches
(GWAS, selection signatures, ‘omics’, bioinformatics)
Validation • Gene editing  performance monitoring
Use

African cattle = unique gene discovery population
Recent study (5 African breeds) identified
selection signatures for:
 Maintaining body weight & resisting anemia
with trypanosome infection (N’dama)
 Feeding behavior
 Heat tolerance
 Tick resistance
Kim et al., 2017
Courtesy James Prendergast

Genomics Reference Resource for African Cattle
Collated and publically available genomic and genetic
information on African cattle – with meta-data
A collaboration between African partners &
CTLGH, with the support of AU-IBAR
Challenge =
access and benefit sharing
agreements
Currently 33 breeds from 13 partner countries

Understanding African cattle adaptation
Proposed portfolio:
 Genotype characterization via on-farm and
on-station trials (evidence base for industry; to
better understand underlying biology feeding into gene
discovery studies)
 Identification of field-measurable proxy traits
(for use in genetic improvement programs  building
resources for genome wide association studies)
Harsh environmental conditions
of cattle rearing (Senegal)

Contributing to productive, profitable and sustainable
dairy cattle production systems, now and in the future
Direct and indirect impacts of climate change on livestock systems
Thornton et al., 2015

www.ctlgh.org