Breeding and genomics in ILRI biosciences research

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.