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• 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

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