Presented by Denis Fidalis Mujibi at the ILRI BioSciences Day, Nairobi, 27 November 2013

1. Use of advanced genomics in determining
appropriate breed types for smallholder dairy
Denis Fidalis Mujibi D.Mujibi@cgiar.org
ILRI BioSciences Day, Nairobi, 27 November 2013

2. Dairy Genetics East Africa Project (DGEA)
• Determine appropriate cattle genotypes for
smallholder dairy farmers in Eastern Africa
• To determine, using advanced genomic approaches, the
underlying breed composition of crossbred dairy cattle in Kenya
and Uganda in relation to appropriate production systems
• To evaluate the ability of diagnostic molecular markers to correctly
assign breed composition to cattle of unknown breed percentages
in smallholder farming systems.

3. Background & Methods
• Methods
• In-situ animal evaluation, Long term productivity data
•
•
•
•
collection in smallholder farms
Collection of socio-economic data through surveys and other
participatory approaches
Genotyping with Illumina HD SNPChip (>700,000 SNPs)
Aligned to CRP 3.7, output 2.1.2.1.2. Beneficiaries: Farmers,
policy makers, Breeders, AI inseminators, NGOs
Matching genotypes to environment increases productivity,
maximizing input: output ratio

4. Results
• Research results
IT WORKED!
Breed composition
• Clear separation of admixed cows
• Genetic architecture of breeds
• Bulk of cows have high exotic signature

5. Results
• Research results
10.00
8.00
6.00
HEL1
4.00
HEL2
2.00
HEL3
0.00
Ave
1
2
3
4
5
Dairy group
Daily milk yield (l/d)
Daily milk yield (l/d)
• Milk yields
8
6
Group 1
4
Group 2
2
Group 3
0
Group 4
1
2
3
4
Group 5
Lactation stage (100 day intervals)
• Attritions and disease
• Very high cow turn over, high trading rates
• ECF and Mastitis prevalent in all sites. TB and Tryps important
for specific sites

6. Conclusions and discussion points
• SNPs able to differentiate various breed types and
grades. Low correlation between farmer assigned breed
composition and SNP derived breed composition (r=0.4)
• There was interaction between production environment
and Breed type
• Very high cow turn-over, implying that genetic delivery
platforms have to factor this in design
150
60
40
20
0
9
Cows
Cows 52 55 48 32 21 55 27 48 44
Males
1
2
Males 11 9
3
7
4
7
5
3
6
7
8
9 13 9
Longitudinal Survey Round
4
Number of Animals
Number of Animals
Animal Acquisitions
Animal Disposals
100
50
0
Cows
Cows
1 2 3 4 5 6 7 8 9
1 1 8 7 4 8 6 9 6
Males 3 3 3 2 1 3 2 3 1
Longitudinal Survey Round
Males

7. Where to from now?
Farmers, NARS, ILRI, KAGRC (PEARLS)
Best matched Bulls/Semen
Breeders, NGOs (NSF BREAD)
Available Bulls/Semen
Dead cows/calves
NARS, ILRI(AgriTT)
Appropriate cows
Selected unhappy lot
Existing cows/imports
Phenotyping
Genotyping
Poor yields
Extension
Feedback
Genetic
Evaluation
Farm Typing
Selective
Breeding
Better yields/more income

8. Grants & Future activities
• Low density SNP chip for SNP composition
assays, parentage testing and ‘appropriateness’ typing
• Adoption of ICT technologies (SMS platforms etc.) for
field data acquisition and feedback (Financial support
required)
• Genotypic diversity in relation to disease burden
(serum/plasma screens for pathogens/parasites)
• Rumen microflora diversity and relation to adaptation
characteristics and diet offered, feed efficiency and GHG
emissions

9. better lives through livestock
ilri.org
The presentation has a Creative Commons licence. You are free to re-use or distribute this work, provided credit is given to ILRI.