Basic HTML Version
Molecular Plant Breeding 2013, Vol.5, No.9, 47
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63
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58
markers
are
not
able
to
provide
precise
and
complete
information
about
the
numbers
and
locations
of
the
genes
and
QTL
controlling
target
traits.
All
the
QTLs
identified
in
the
study
were
under
hydroponic
conditions
and
need
to
be
confirm
under
natural
saline
field
if
it
will
be
stable
or
different
as
none
of
the
QTLs
designated
as
the
most
significant
under
field
conditions
do
not
seems
to
co-localized
with QTLs
detected
under
hydroponics
(Negrao
et
al.,
2011).
Similar
observations
have
also
been
made
in
barley
where
salinity
stress
was
shown
to
have
a
different
impact
in
plants
grown
under
hydroponics
and
soil
systems
(Tavakkoli
et
al.,
2010).
3 Conclusions
The
performance
of
the
31
RILs
based
on
SES
score
similar
to
or
better
than
Hasawi
the
tolerant
parent
and
also
having
other
important
traits
studied will
be
further
evaluated
in
fields
heavily
affected
by
salinity.
The
SNP
markers
nearest
to
the
seven
QTLs
associated
with
salt-tolerant
traits
will
be
useful
for
marker-aided
breeding
targeting
rice
cultivars
for
saline-prone
environments.
There
is
the
need
to
identify
rice
cultivars
or
breeding
lines
differing
only
in
the
presence
of
a
single
and
specific QTL
for
shoot
growth
and
plant
height
under
saline
stress
to
precisely
map
genes
controlling
each
trait
and
to
elucidate
the
biological
functions
of
these
QTL.
This
knowledge
about
QTL
controlling
salt
tolerance
will
be
valuable
for
plant
breeders
developing
high-yielding
rice
cultivars
aiming
farming
systems
affected
by
salinity.
4 Materials
and
Methods
Two
experiments were
conducted:
one
in
a
screenhouse
and
other
at
the
laboratory.
The
screenhouse
experiment was
at Africa Rice
Sahel Regional
Station
near
Saint
Louis
Senegal,
The
DNA
extraction
was
done
in
the
Biosciences
Eastern
and
Central
Africa
BecA,
laboratory
based
at
the
International
Livestock
Research
Institute
ILRI,
in
Nairobi
Kenya,
while
the
SNP
genotyping
and
analysis
were
at
IRRI
in
Los
Baños,
The
Philippines.
4.1 Screening
for
salt
tolerance
This
experiment
to
evaluate
salt
tolerance
at
the
seedling
stage was
carried
out
in
2012
using
300
F
5:6
RILs,
which
were
derived
from
IR29×Hasawi
cross,
following
the
method
described
by
Gregorio
et
al.
(1997),
IR
29
Acc
No.
IRGC
30412,
is
IRRI
developed
variety
and
Hasawi
Acc
No.1681,
is
a
landrace
from
eastern
Saudi Arabia. The
experimental
layout was
a
randomized
complete
block
design with
three
replications
two
for
salinity
stress
and
one
as
non-saline
control,
Salinized
Yoshida’s
solution
(Yoshida
et
al.,
1976), with
slight modifications
as
per
the
protocol
by
Singh
and
Flower
(2011),
replaced
the
distilled
water
3
days
after
in
the
replications
under
saline
stress.
The
initial
salinization
was
maintained
at
an
electrical
conductivity
EC,
of
6
dSm
-1
after
adding
approximately
5.13mM
to
the
solution.
This
concentration was
increased
to
12
dSm
-1
after
3
days
of
being
under
the
6
dSm
-1
treatment
to
reduce
the
immediate
shock.
The
pH
of
the
nutrient
solution was
maintained
at
approximately
5
and
the
solution
renewed
weekly
throughout
the
experiment.
We
took
three
plants
to
rate
their
response
to
salinity
using
the
standard
evaluation
score
SES
(IRRI,
1996),
and
to
measure
their
shoot
fresh
weight,
shoot
dry
weight
plus
root
and
shoot
length.
The
corner
plant
was
left
in
every
replication.
The
initial,
2
nd
and
3rd
SES
rating were
done
as
per
the
protocol
of Gregorio
et
al.
(1997),
shoot
and
root
length,
as
well
as
shoot
dry
and
fresh
root
weight
were
measured
after
the
final
SES
reading.
Both
the
shoot
dry
and
root
dry
weight were
recorded
after
drying
samples
in
an
oven
at
60°C
for
3
days.
IR29
and
Hasawi
were
the
susceptible
and
tolerant
checks
respectively,
in
this
screening
trial.
Data
were
analyzed
with Windowstat
version
8.5
while
SPSS
16.0
was
used
for
both
diagrams
and
charts.
4.2 Selection
Criteria
for
Molecular
and
QTL
Detection
Genotyping was
carried
out
using
the
extremes
of
F5
RILs
that
performed
better
and
poorly
based
on
combination
of
SES
final
scores
as well
as
shoot
fresh
and
dry
weight
measured
in
the
F
5:6
RILs.
To
eliminate
biasness,
we
randomly
selected
some
intermediate
RILs
from
the
population
and
added
to
the
RILs
for
the
SNP
analysis.
A
total
of
142
RILs
from
the
300
were
selected
and
used
in
this
study.
4.3 DNA
Extraction
Genomic
DNA
was
extracted
from
young
leaves
of
two
plants
of
each
parent
and
one
plant
each
of
the
142
F
5
RILs
using
the
protocol
of
Dellaporta
et
al