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Breeding and genomics in ILRI biosciences research

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Presented by Steve Kemp at the ILRI BioSciences Day, Nairobi, 27 November 2013 …

Presented by Steve Kemp at the ILRI BioSciences Day, Nairobi, 27 November 2013


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  • 1. Breeding and genomics in ILRI biosciences research Steve Kemp ILRI BioSciences Day, Nairobi, 27 November 2013
  • 2. Livestock diversity
  • 3. Livestock diversity Genome sequence determines characteristics: • Disease resistance • Drought tolerance • Productivity
  • 4. Livestock diversity Genome sequence MOSTLY determines characteristics, but what determines productivity in a given system? • • • • Genetics ? Feed ? Health ? Management ? That is a meaningless question!
  • 5. Disease resistance Boran N’Dama Bovins Cattle Glossines Tsetse Bovins et Glossines Cattle and tsetse
  • 6. Contribution of 10 genes from Boran and N’Dama cattle to reduction in degree of trypanosomosis Boran (relatively susceptible) 15 10 5 0 -5 -10 -15 N’Dama (tolerant) 15 10 5 0 -5 -10 -15 The N’Dama and Boran each contribute trypanotolerance alleles at 5 of the 10 most significant QTL, indicating that a synthetic breed could have even higher tolerance than the N’Dama.
  • 7. Alignment of N’Dama ARHGAP15 with homologues H P mutation at AA282 Cow NDama KFITRRPSLKTLQEKGLIKDQIFGSPLHTLCEREKSTVPRFVKQCIEAVEK Cow Boran KFITRRPSLKTLQEKGLIKDQIFGSHLHTLCEREKSTVPRFVKQCIEAVEK Human KFISRRPSLKTLQEKGLIKDQIFGSHLHTVCEREHSTVPWFVKQCIEAVEK Pig Chicken KFITRRPSLKTLQEKGLIKDQIFGSHLHTVCERENSTVPRFVKQCIEAVEK KFISRRPSLKTLQEKGLIKDQIFGSHLHLVCEHENSTVPQFVRQCIKAVER Salmon KFISRRPSMKTLQEKGIIKDRVFGCHLLALCEREGTTVPKFVRQCVEAVEK N'Dama (n = 35) Boran (n = 28) Gene frequency 282P-Allele 0.990 0.125 282H-Allele 0.010 0.875
  • 8. Alignment of N’Dama ARHGAP15 with homologues That mutationof AA282 H P piece at work took a lot of time and money. Cow NDama What has it really achieved? KFITRRPSLKTLQEKGLIKDQIFGSPLHTLCEREKSTVPRFVKQCIEAVEK Cow Boran KFITRRPSLKTLQEKGLIKDQIFGSHLHTLCEREKSTVPRFVKQCIEAVEK Human KFISRRPSLKTLQEKGLIKDQIFGSHLHTVCEREHSTVPWFVKQCIEAVEK Pig Chicken KFITRRPSLKTLQEKGLIKDQIFGSHLHTVCERENSTVPRFVKQCIEAVEK KFISRRPSLKTLQEKGLIKDQIFGSHLHLVCEHENSTVPQFVRQCIKAVER Salmon KFISRRPSMKTLQEKGIIKDRVFGCHLLALCEREGTTVPKFVRQCVEAVEK N'Dama (n = 35) Boran (n = 28) Gene frequency 282P-Allele 0.990 0.125 282H-Allele 0.010 0.875
  • 9. The technology behind such ‘gene discovery’ has been transformed
  • 10. The technology behind such ‘gene discovery’ has been transformed
  • 11. The technology behind ‘gene delivery’ has NOT been transformed It is not rocket science! But that does not mean it is easy.. …and we need a complete pipeline
  • 12. The pipeline is therefore incomplete Genome sequence is now easy to obtain. Phenotype information is now HARDER to obtain. We need both.
  • 13. The technology behind ‘gene delivery’ has NOT (entirely) been transformed TALENS technology. Is somewhere along that pipeline and allows us to perform ‘precision crossbreeding’, or gene editing. We can now swap alleles at 100 genes in one go. But we don’t have 100 candidate SNPs, because the pipeline is dry. But we do have 2! We need to re-establish a genetics pipeline.
  • 14. We need to re-establish a genetics pipeline Sequence Conserve Phenotype Function Deliver to an animal Deliver to the user What traits? What species? What breeds? What target systems? Where to look for variation?
  • 15. Livestock diversity A cow is mostly non-cow: •Rumen sequence PARTLY Genome •Skin determines characteristics: •Milk • Disease resistance •Soil • Drought tolerance • Productivity Metagenomes play a role and interact with each other. So ‘describing a cow, suddenly became much more fun.