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

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.

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

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

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

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

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

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

better lives through livestock
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