Presented by Karen Marshall, ILRI, and Eileen Wall, Scotland's Rural College, at the CTLGH Project Management Committee Meeting, Edinburgh, 19-20 April 2017

1. Dairy Genomics Program of
the Centre for Tropical
Livestock Genetics and Health
Tropical Dairy Genomics
Karen Marshall, ILRI
Eileen Wall, Scotland's Rural College
CTLGH Project Management Committee
Meeting, Edinburgh, 19-20 April 2017

2. Dairy Genomics Intermediate Outcome 1.1:
- [current] 5 proof of concept genomic/
metagenomic predictions or algorithms
developed and tested for at least 2 tropical
adaptability and resilience traits to aid the
selection of superior locally adapted breeding
bulls for use in Africa.
(restricts technology options)
- [suggested] n proof of concept genomic based
technologies to aid the selection of superior
locally adapted breeding bulls for use in Africa.
CTLGH-BMGF-DFID results tracker (March 2017)
Simultaneously genetic
improvement programs
need to be developed to
take advantage of these
technologies.
Need to take care that
what is produced will be
in demand by
stakeholders

3. Define and characterize at least 5 tropical cattle adaptability/resilience
traits such as heat stress, lactation persistency, tropical cow fertility and
efficiency of local fodder utilization. UNDERPINS ALL OTHER OUTPUTS
Heat stress, efficiency of local fodder utilization
 No phenotypic data exists or currently being collected
 Research infrastructure required (ILRI’s Kapiti farm)
Lactation persistency, tropical cow fertility
 Phenotypic data being collected by ADGG, sufficient by early 2019
Other - general disease resistance tolerance; fertility status particularly pregnancy;
energy status including metabolic disorder
 Additional data collection activities linked to ADGG
 Novel phenomics to be developed to facilitate process
Output 1.1.1
Proposal
feed - heat -
milk
Proposal
novel
phenomics
Proposal
ADGG
interface

4. Key research facilities required
Equip the ILRI Kapiti station (32,000 Acres in semi-arid environment,
currently running 2200 cattle and 1600 small ruminants) with:
 Dairy shed with automatic milkers
 Ability to measure feed intake (e.g. Growsafe)
 Climate options (shade)
 Various for specific tests
Proposal
novel
phenomics
Proposal
feed - heat -
milk

5. Step 1: Identify potential associations
 Genomics Reference Resource for African Cattle
 Sequence information + geo-reference co-ordinates
 Can explore data for ‘signatures of selection’ for traits e.g.
temperature (but power unknown)
 ADGG
 Can perform association studies when discovery
population is sufficiently large
 Other data via new projects
Output 1.1.2
Proposal
novel
phenomics
Proposal
ADGG
interface
Generate high resolution genotypes and phenotypes on local and exotic cattle
and confirm associations of at least 10 putative causal variants linked to selected
traits of tropical adaptability and resilience.
Proposal
feed - heat -
milk

6. Step 2: Confirm associations
 Various approaches; timely (beyond 2020)
 Direct and correlated effects need to be evaluated for use in breeding programs
(suggest output is reworded to include productivity under local environments and omit step 2)
Output 1.1.2
Generate high resolution genotypes and phenotypes on local and exotic cattle
and confirm associations of at least 10 putative causal variants linked to selected
traits of tropical adaptability and resilience.

7. Transfer at least 5 genomic/metageomic prediction algorithms for use in the
African Dairy Genetic Gain program.
Output 1.1.3
 ADGG is employing genomic selection and thus will
be developing prediction algorithms to select
breeding animals within their population - CTLGH
can assist by strengthening the genomic and
phenomic data
 Both CTLGH and ADGG have activities around a
‘smart tool for breed composition’ and can
collaborate here
Proposal
novel
phenomics
Proposal
ADGG
interface
(output rewording suggested to capture collabotative nature of ADGG – CTLGH rather than
transfer; genomic tools rather than algorithms; potential use of tools outside of ADGG)
Proposal
ADGG
interface

8. Output 1.1.4
Transfer 5 well-characterized tropical cattle adaptability and resilience
genetic/ metagenomic variants to program 03 for further development
into precision breeding tools.
 Confirmation of (some of) the
putative causal variants identified
by the program will be beyond
2020
 Can focus on existing (literature)
options – e.g. trypanotolerance
(Babboon ApoL1); ECF resistance
(in discovery)
(suggest revise output wording from transfer to identify to reflect that the
variants may arise from literature rather than program activities; also
proof of concept rather than development into precision breeding tools)

9. Summary
1.1.1
New knowledge on
adaptation
1.1.2
Identification of
putative causal
variants
1.1.3 Tools /
algorithms for
strengthened
genetic
improvement
programs
OUTPUTS
INTERMEDIATE
OUTCOMES
ACTIVITIES / PROJECTS
1.1
Proof of concept
genomic based
technologies to aid the
selection of superior
locally adapted breeding
bulls for use in Africa
Enhanced genomic tools
 Genomics Reference Resource for
African cattle
 Low-cost genotyping platform
 Smart tool for breed composition
NEW: ‘Feed – heat – milk’
NEW: ‘Novel phenomics’
NEW: ‘ADGG interface’
Selection signatures for traits of
interest (building on the Genomics
Reference Resource)

10. ‘Feed – Heat – Milk’ deliverables
General idea: Characterize the interaction between feed
efficiency, heat stress and milk production for dairy
cattle with different proportions indigenous / exotic
Deliverables
 Assessment of key genotype by environment
(GxE) interactions relevant to dairy cattle
production in Africa
 Initial data towards identification of causal
variants
 Practical recommendations at various levels -
policy makers, breeding program implementers,
farmers
Ballpark budget: 2-3m USD (due to need for facilities)
Could potentially expand to include rumen microbiome characterisation

11. ‘Novel Phenomics’ deliverables
General idea: develop field-suitable novel
phenomics on-station and introduce into ADGG
to strengthen its program
Deliverables
 New phenomic tools pilot-tested in-situ
 ADGG field recording program extended
to new traits
 Enhanced ADGG selection algorithms
 Undertaken gene discovery activities on
key adaptability traits
Ballpark budget: 0.5m USD

12. ‘ADGG Interface’ deliverables
General idea: Leverage of CTLGH and ADGG investments through a set of 4
activities (see CN)
Deliverables
 Reduced SNP sets for breed composition and gEBV estimates* for any
African population *when combined with reference population data
 Known limits of breed composition tool to refine to underlying breeds
(rather than breed-groups e.g. Zebu, Taurus)
 Undertaken gene discovery activities for milk productivity & other
traits at higher accuracy than currently possible
 Understanding of breed effect on calf mortality, and undertaken gene
discovery activities for calf mortality

13. ‘ADGG Interface’ deliverables
General idea: Leverage of CTLGH and ADGG investments through a set of 4
activities (see CN)
Deliverables
 Reduced SNP sets for breed composition and gEBV estimates* for any
African population *when combined with reference population data
 Combine ADGG, SDG and CTLGH (Malawi) data; additional genotyping + analysis
needed
 Known limits of breed composition tool to refine to underlying breeds
(rather than breed-groups e.g. Zebu, Taurus)
 Use of commercial dairy data with known breed proportion; additional genotyping
+ analysis needed
 Undertaken gene discovery activities for milk productivity & other
traits at higher accuracy than currently possible
 Extend ADGG genotyping to HD: additional genotyping + analysis needed
 Understanding of breed effect on calf mortality, and undertaken gene
discovery activities for calf mortality
 Extend ADGG phenotyping to follow calves for first year of life; additional
phenotyping, genotyping + analysis needed

14. 1.1 2 proof of concept genomic based technologies to aid the
selection of superior locally adapted breeding bulls for use in Africa
1.1.1 Define and characterize at least 2 cattle adaptability/resilience or
productivity traits such as heat tolerance, lactation persistency, tropical cow
fertility and efficiency of local fodder utilization
1.1.2 Generate high resolution genotypes and phenotypes on local and exotic
cattle and identify at-least 5 putative causal variants linked to cattle
adaptability/resilience or productivity traits
1.1.3 In collaboration with the African Dairy Genetics Gain (ADDG) program
develop genomic tools and/or prediction algorithms to aid the selection of
superior dairy cattle
1.1.4 Identify (including from literature) 5 cattle adaptability/resilience or
productivity genetic/ metagenomic variants for program 03 to use as proof of
concept in relation to producing gene-edited cattle
Target numbers still to be discussed
Suggested revised outcomes and outputs

15. 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.
CTLGH Dairy Genomics Program co-leads
 Karen Marshall, the International Livestock Research Institute, kmarshall@cgiar.org.
 Eilleen Wall, Scotland’s Rural College, Eileen.Wall@SRUC.ac.uk