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Presented by Steve Kemp at the ILRI BioSciences Day, Nairobi, 27 November 2013
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Breeding and genomics in ILRI biosciences
researchSteve Kemp
ILRI BioSciences Day, Nairobi, 27 November 2013
Livestock diversity
Livestock diversity
Genome sequence determines characteristics:• Disease resistance• Drought tolerance• Productivity
Livestock diversity
Genome sequence MOSTLY determines characteristics, but what determines productivity in a given system?
• Genetics ?• Feed ?• Health ?• Management ?
That is a meaningless question!
CattleTsetseCattle and tsetse
Disease resistance
N’DamaBoran
Contribution of 10 genes from Boran and N’Dama
cattle to reduction in degree of trypanosomosis
Boran (relatively susceptible)
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.
N’Dama (tolerant)
Gene frequency
H P mutation at AA282
Alignment of N’Dama ARHGAP15 with homologues
Cow NDama KFITRRPSLKTLQEKGLIKDQIFGSPLHTLCEREKSTVPRFVKQCIEAVEK
Cow Boran KFITRRPSLKTLQEKGLIKDQIFGSHLHTLCEREKSTVPRFVKQCIEAVEK
Human KFISRRPSLKTLQEKGLIKDQIFGSHLHTVCEREHSTVPWFVKQCIEAVEK
Pig KFITRRPSLKTLQEKGLIKDQIFGSHLHTVCERENSTVPRFVKQCIEAVEK
Chicken KFISRRPSLKTLQEKGLIKDQIFGSHLHLVCEHENSTVPQFVRQCIKAVER
Salmon KFISRRPSMKTLQEKGIIKDRVFGCHLLALCEREGTTVPKFVRQCVEAVEK
Gene frequency
H P mutation at AA282
Alignment of N’Dama ARHGAP15 with homologues
Cow NDama KFITRRPSLKTLQEKGLIKDQIFGSPLHTLCEREKSTVPRFVKQCIEAVEK
Cow Boran KFITRRPSLKTLQEKGLIKDQIFGSHLHTLCEREKSTVPRFVKQCIEAVEK
Human KFISRRPSLKTLQEKGLIKDQIFGSHLHTVCEREHSTVPWFVKQCIEAVEK
Pig KFITRRPSLKTLQEKGLIKDQIFGSHLHTVCERENSTVPRFVKQCIEAVEK
Chicken KFISRRPSLKTLQEKGLIKDQIFGSHLHLVCEHENSTVPQFVRQCIKAVER
Salmon KFISRRPSMKTLQEKGIIKDRVFGCHLLALCEREGTTVPKFVRQCVEAVEK
That piece of work took a lot of time and money.
What has it really achieved?
That piece of work took a lot of time and money.
What has it really achieved?
The technology behind such ‘gene discovery’ has been transformed
The technology behind such ‘gene discovery’ has been transformed
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
It is not rocket science!
But that does not mean it is easy..
…and we need a complete pipeline
The pipeline is therefore incomplete
Genome sequence is now easy to obtain.
Phenotype information is now HARDER to obtain.
We need both.
Genome sequence is now easy to obtain.
Phenotype information is now HARDER to obtain.
We need both.
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.
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.
We need to re-establish a genetics pipeline
Sequence
Conserve
Phenotype
Function
Deliver to an animal
Deliver to the user
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?
What traits?What species?What breeds?What target systems?Where to look for variation?
Livestock diversity
Genome sequence PARTLY determines characteristics:• Disease resistance• Drought tolerance• Productivity
A cow is mostly non-cow:• Rumen• Skin• Milk• Soil
Metagenomes play a role and interact with each other.
So ‘describing a cow, suddenly became much more fun.
A cow is mostly non-cow:• Rumen• Skin• Milk• Soil
Metagenomes play a role and interact with each other.
So ‘describing a cow, suddenly became much more fun.