Finding good and bad genes in Boran
and N’Dama genome sequences
What makes Boran more susceptible to trypanosomiasis than N’Dama?
Trinity College Dublin
Boran (relatively susceptible) N’Dama (tolerant)
Cow Chromosomes
PCV
Body
weight
Parasitaemia
Hano5e
et
al
PNAS
2003
7443-­‐7448
Boran cattle are much more susceptible to to trypanosomiasis than N’Dama. The gene mapping studies at The black bars represent the 29 autosomes and two sex chromosomes of cattle.
ILRI in Nairobi showed that genes at ten places in the genome controlled the response to infection. A Coloured bars represent the position of the ten regions of the genome that contain genes
surprising observation was that both Boran and N’Dama had ‘Good’ and ‘Bad’ genes. The graphs under that make a difference to how N’Dama and Boran respond to infection. Red, blue and
each animal show the effect of the ‘Bad’ genes below the midline and the effect of the ‘Good’ genes above pale blue bars show where there are genes controlling anemia, body weight and
the midline. The difference between the two breeds is that the ‘Good’ genes in N’Dama have a larger effect parasitaemia after infection. Each of the coloured bars cover 20-100% of a chromosome;
relative to the ‘Bad’ ones than Boran. these regions contain many genes making it difficult to identify the genes that make the
difference.
Next Generation sequencing to the rescue
DNA differences that effect phenotype
Next generation sequencing is transforming
genetics. One ABI SOLiD instrument can generate Consequence of Polymorphism N'Dama Boran Sahiwal
50Gb of sequence in a run, compared to only 3Gb 3 PRIME UTR 16,786 10,311 30,733
in a human or cow genome. That means we can 5 PRIME UTR 3,885 1,601 6,651
sequence each genome many times over to ensure DOWNSTREAM 7,398 4,536 16,497
highly accurate detection of differences between ESSENTIAL SPLICE SITE 2 267 1,029
breeds.
INTRONIC 37,758 2,223 35,803
We have sequenced DNA from 10 Boran from the NON SYNONYMOUS CODING 29,350 10,454 45,344
ILRI ranch at Kapiti and 20 N’Dama from Guinea to SPLICE SITE 2,044 592 7,674
discover the majority of the common differences STOP GAINED 935 145 1,344
between these breeds.
STOP LOST 25 11 41
We can then look within the regions of the genome SYNONYMOUS CODING 32,404 17,516 61,491
where we know that there are good trypanosomiasis UPSTREAM 4,974 1,948 10,867
genes in one breed or bad genes in the other and WITHIN MATURE miRNA 10 6 41
find differences within genes that could have an WITHIN NON CODING GENE 2,331 1,308 4,855
important effect on their phenotype.
Table of the number of SNP with each type of effect on gene function.
In addition to Boran and N’Dama we have also sequenced Sahiwal, a pure Bos indicus
breed. Polymorphisms are differences between two DNA sequences. Only about 2% of
DNA codes for genes, the rest either regulates when and where genes are switched on
or they have no obvious purpose.
The differences between sequences that are most likely to effect an animal’s phenotype
are within genes. And within genes the most important differences are ones that cause a
difference in the protein sequence (NON SYNONYMOUS CODING) or effect how the
components of the gene are assembled (ESSENTIAL SPLICE SITE) or disrupt a gene
altogether (STOP GAINED), and these are highlighted in the table. We are looking at the
regions of the genome where we know that the good and bad trypanosomiasis
Minor allele frequencies in N’Dama chromosome 16 where there is a ‘good’ gene. resistance genes are, to see which ones have these most important differences in them.
The dips in the graph are regions where there is very little variation in N’Dama, this could have been
caused by selection for a beneficial variant of a gene either by the process of domestication or because We are already testing the effect of a STOP GAINED polymorphism in the PON3 gene
one variant was better at resisting disease than another. The circle highlights the Tlr5 gene that is that could be responsible for large differences in expression of this gene. PON family
important in the innate immune response and could therefore have been selected to resist genes have been shown to effect survival of mice after infection so this difference could
trypanosomiasis and / or other diseases. Less is known about the other genes that appear to be under be important.
selection but they may also be important
The good news is … And the not so good news is …
We
now
have
a
short
list
of
genes
that
might
regulate
response
to
trypanosomiasis
as
There
is
s5ll
a
lot
of
work
to
be
done
to
confirm
which
genes
are
involved
and
how
they
well
as
a
large
set
of
gene5c
markers
for
African
ca9le
that
will
be
valuable
for
future
effect
the
disease
process.
April 2010
research.