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!
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
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.
14. 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.
15. 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?
16. 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.