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Use of advanced genomics in determining appropriate breed types for smallholder dairy
 

Use of advanced genomics in determining appropriate breed types for smallholder dairy

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

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


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  • There MUST be a CGIAR logo or a CRP logo. You can copy and paste the logo you need from the final slide of this presentation. Then you can delete that final slide To replace a photo above, copy and paste this link in your browser: http://www.flickr.com/photos/ilri/sets/72157632057087650/detail/ Find a photo you like and the right size, copy and paste it in the block above.

Use of advanced genomics in determining appropriate breed types for smallholder dairy Use of advanced genomics in determining appropriate breed types for smallholder dairy Presentation Transcript

  • 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 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.