Genomics
capacity
has
been
built
in
the
region.
African
scien7sts
are
now
addressing
African
agricultural
challenges
through
the
use
of
Genomics,
in
house,
since
Genomics
capacity
is
now
available
in
the
region
through
the
BecA-­‐ILRI
Hub.
Advancement
in
African
agricultural
research
and
increased
levels
of
collabora7on
in
the
region.
A
compe77ve,
high-­‐tech
research
Hub
available
to
African
scien7sts
to
solve
African
agricultural
problems.
BecA-­‐ILRI
Hub
Genomics
Pla6orm
and
Applica:ons
The
field
of
Genomics
is
evolving
at
an
extremely
rapid
pace
in
conjunc7on
with
drama7c
reduc7ons
in
the
cost
of
sequencing
per-­‐base
(Fig.
1).
Genomics
holds
the
poten7al
to
develop
and
strategically
deploy
exis7ng
crop
varie7es
and
livestock
breeds
so
that
they
can
thrive
in
the
hos7le
environment
with
harsh
environmental
and
biological
stresses.
A
leading
resource
in
these
efforts,
the
BecA-­‐ILRI
Hub
genomics
plaMorm
avails
low,
medium
and
high
throughput
sequencing
and
analysis
technology
previously
unavailable
to
regional
scien7sts.
Equipped
with
both
capillary
systems,
including
ABI
3130-­‐xl,
ABI
3730-­‐xl
and
ABI
3500-­‐xl,
and
next
genera7on
sequencing
(NGS)
technologies
(Fig.
2),
our
genomics
plaMorm
is
maintained
at
the
cuVng
edge
of
NGS
technology,
specifically
of
relevance
to
the
efforts
of
African
Hub
users.
Driven
by
regional
demand,
in
2013
we
acquired
the
first
Illumina
genome
sequencing
machine
(Illumina
MiSeq)
in
the
region.
The
high
request
in
its
use,
received
from
regional
users
and
partners,
translated
into
the
acquisi7on
of
a
second
Illumina
MiSeq
System
in
2014.
The
MiSeq
Systems
have
increased
our
sequencing
throughput
and
complemented
the
Sequencing,
Genotyping,
OligoSynthesis
and
Proteomics
(SegoliP)
service
Unit
in
its
effort
to
serve
the
region
while
significantly
reducing
our
per-­‐base
sequencing
costs.
Plans
for
NGS
service
provision
are
ongoing
and
our
service-­‐based
ac7vi7es
will
start
in
the
first
quarter
of
2016.
The
BecA-­‐
ILRI
Hub
Genomics
plaMorm
is
strictly
linked
with
the
BecA-­‐ILRI
Hub
Bioinforma7cs
plaMorm
in
order
to
give
the
users
data
analysis
support
a^er
data
genera7on.
This
document
is
licensed
for
use
under
a
Crea7ve
Commons
A`ribu7on
–Non
commercial-­‐Share
Alike
3.0
Unported
License
February
2016
Genomics
Partnerships
Outcomes
Outputs
Figure
1:
Evolu7on
of
sequencing
instruments
and
drop
in
price
over
7me,
from
capillary
technologies
through
Second
(Roche
454)
un7l
Next
Genera7on
Sequencing
(NGS)
Technologies
(Illumina).
Figure
2:
The
BecA-­‐ILRI
Hub
Genomics
PlaMorm
is
equipped
with
both
Capillary
and
Next
Genera7ons
Sequencing
(NGS)
machines.
Two
Illumina
MiSeq
Systems
acquired
in
2013
and
in
2014
have
significantly
increased
our
Genomics
capacity
and
throughput
while
reducing
our
sequencing
costs.
The
BecA-­‐ILRI
Hub
Genomics
plaMorm
has
been
used
to
address
several
agricultural
challenges
related
with
food
safety
and
security
in
the
region
and
beyond.
Some
of
the
applica7ons
include:
crop
and
livestock
improvement,
transcriptomic,
viral
discovery,
disease
diagnos7cs,
whole
genome
sequencing,
etc.
We
have
generated
1.1
terabytes
of
NGS
sequence
data
since
2013.
BecA-­‐ILRI
Hub
staff
and
more
than
20
African
scien7sts
have
been
mentored
and
trained
in
the
use
of
the
genomics
plaMorm
at
the
BecA-­‐ILRI
Hub,
through
targeted
training
and
workshops.
Capillary
Sequencing
Next
genera:on
Sequencing
The
BecA-­‐ILRI
Hub
Genomics
plaMorm
has
seen
an
exponen7al
request
and
demand
from
CGIAR
partners
and
Na7onal
partners
during
the
last
two
years.
For
this
reason
plans
are
in
place
for
the
establishment
of
service
provision
in
2016.
The
established
collabora7ons
with
Na7onal
and
Interna7onal
users
have
allowed
the
op7miza7on
and
improvement
of
several
Genomics
ac7vi7es
and
applica7ons.
We
will
be
able
to
offer
Genotyping
by
Sequencing
(GBS)
exper7se
and
training
in
the
near
future
to
all
our
partners
and
users.
Poten7al
to
scale-­‐up
Partnerships
with
Na7onal
Agricultural
Research
Systems
(NARS)
in
the
BecA
region
and
beyond
(e.g.
MARI,
RAB,
etc.)
have
been
established
and
will
form
the
base
for
future
collabora7ons
in
need
of
Genomics
exper7se
and
capacity
building.
Partnerships
with
Interna7onal
organiza7ons
(e.g.
FERA,
JIC,
etc.)
have
been
created
to
deliver
targeted
training
in
Genomics
applica7ons
and
protocol
development.
Francesca
Stomeo
or
Josephine
Birungi
F.Stomeo@cgiar.org,
J.Birungi@cgiar.org
●
hub.africabiosciences.org
Funding:
Swedish
Government