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Presented by Denis Fidalis Mujibi at the ILRI BioSciences Day, Nairobi, 27 November 2013
Citation preview
Use of advanced genomics in determining appropriate breed types for smallholder dairy
Denis Fidalis Mujibi [email protected]
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• Milk yields
• 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
1 1.5 2 2.5 3 3.5 4 4.5 50.00
2.00
4.00
6.00
8.00
10.00
HEL1HEL2HEL3Ave
Dairy group
Daily
milk
yie
ld (l
/d)
1 2 3 40
2
4
6
8
Group 1Group 2Group 3Group 4Group 5
Lactation stage (100 day intervals)
Daily
milk
yie
ld (l
/d)
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
1 2 3 4 5 6 7 8 9
Cows
52 55 48 32 21 55 27 48 44
Males
11 9 7 7 3 9 13 9 4
535
Animal Acquisitions
CowsMales
Longitudinal Survey Round
Num
ber o
f Ani
mal
s
1 2 3 4 5 6 7 8 9
Cows
133
100
89 72 49 86 62 97 64
Males
34 36 30 21 11 34 24 30 14
1070
130
Animal Disposals
CowsMales
Longitudinal Survey Round
Num
ber
of A
nim
als
PhenotypingGenotyping
Farm Typing
Selective Breeding
Genetic Evaluation
ExtensionFeedback
Farmers, NARS, ILRI, KAGRC (PEARLS)
Breeders, NGOs (NSF BREAD)
NARS, ILRI(AgriTT)
Where to from now?
Existing cows/imports
Dead cows/calves
Selected unhappy lot
Poor yields Better yields/more income
Appropriate cows
Best matched Bulls/Semen
Available Bulls/Semen
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
The presentation has a Creative Commons licence. You are free to re-use or distribute this work, provided credit is given to ILRI.
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