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Molecular Plant Breeding 2013, Vol.5, No.9, 47
-
63
http://mpb.biopublisher.ca
47
Research
Report
Open
Access
Mapping QTLs
Related
to
Salt
Tolerance
in
Rice
at
the
Young
Seedling
Stage
using
384-plex
Single
Nucleotide
Polymorphism
SNP,
Marker
Sets
Isaac Kofi Bimpong
1
, Baboucarr Manneh
1
, Raafat
El-Namaky
1
,
Faty Diaw
1
, Nana Kofi Abaka Amoah
1
,
Bakary
Sanneh
1
,
Kanfany
Ghislain
1
,
Abdulai
Sow
1
,
R.K.
Singh
2
,
Glenn
Gregorio
2
,
Jean
Berchmans
Bizimana
3
,
M.
Wopereis
4
1.
Africa
Rice
Centre,
Sahel
Regional
Station,
B.P
96,
Saint
Louis,
Senegal
2.
International
Rice
Research
Institute
IRRI),
DAPO
Box
7777,
Metro
Manila,
Philippines
3.
Tanzania
National
Agricultural
Research
Institute
4.
Africa
Rice
Centre,
01
BP
2031,
Cotonou,
Benin
Corresponding
authors
email:
kofibimpong@yahoo.com
Authors
Molecular
Plant
Breeding,
2014,
Vol.5,
No.9
doi:
10.5376/mpb.2014.05.0009
Received:
19
May.,
2014
Accepted:
28
May,
2014
Published:
13
Jun.,
2014
Copyright
©2014
Bimpong
et
al.,
This
is
an
open
access
article
published
under
the
terms
of
the
Creative
Commons
Attribution
License,
which
permits
unrestricted
use,
distribution,
and
reproduction
in
any
medium,
provided
the
original
work
is
properly
cited.
Preferred
citation
for
this
article:
Bimpong
et
al.,
Mapping
QTLs
Related
to
Salt
Tolerance
in
Rice
at
the
Young
Seedling
Stage
using
384-plex
Single
Nucleotide
Polymorphism
SNP,
Marker
Sets,
Molecular
Plant
Breeding,
2014,
Vol.5,
No.
9
47
-
63
(doi:
10.5376/mpb.2014.05.0009)
Abstract
Salinity
is
one
of
the most
serious
factors
limiting
the
productivity
of
rice
crops, with
adverse
effects
on
germination,
plant
vigor
and
crop
yield.
A
population
of
300
F
5:6
recombinant
inbred
lines
RILs),
which
was
derived
from
a
cross
between
IR29
indica
sensitive
to
salinity,
and
Hasawi
Saudi
cultivar
showing
salt
tolerance),
was
evaluated
at
a
young
seedling
stage
under
hydroponic
conditions
at
an
EC
of
12
dsm
-1
.
Such
RIL
population
when
fixed
can
be
repeatedly
used
for
investigating
QTLs
of
various
phenotypes
under
different
environments.
Transgressive
segregation
was
noted
for
all
traits
in
the
RILs;
In
all
31
RILs
10%
of
the
300
RILs,
had
tolerance
level
similar
or
better
than
Hasawi
as
determined
by
their
standard
evaluation
system
SES,
score
of
4
or
less,
performance
under
both
saline
and
non-saline
conditions
for
plant
height,
root
length,
shoot
dry
weight
and
shoot
fresh
weight;
suggesting
these
RILs
can
be
rated
as
tolerant
to
salinity
and
are
been
advanced
in
our
breeding
program.
Quantitative
trait
loci
QTL,
related
to
salt
tolerance
were
detected
using
142
F
5
RILs
and
single
nucleotide
polymorphisms
SNPs,
chip
composed
of
384
SNP
markers
for
indica
×
indica
background.
There
were
seven
significant
QTL
related
to
4
different
traits
associated
to
salt
tolerance
at
young
seedling
stage.
They
were
mapped
on
chromosomes
1,
2
and
6.
The QTL
qDW1.1,
qDW2.1,
qDW2.2
and
qDW6.1
co-segregated with
shoot
dry weight
and
accounted
between
10.6
and
42.3%
of
its
phenotypic
variation,
while
qPH1.1
and
qPH1.2
were
associated
with
plant
height
explaining
between
12.7
and
13.8%
of
its
phenotypic
variation),
and
qF2.1
co-segregated
with
shoot
fresh
weight
10.6%
of
trait
variation,
was
accounted
by
SNP
marker
id2007526,
These
QTLs
had
positive
additive
effects
confirming
that
Hasawi
alleles
contributed
to
enhance
traits
related
to
salt
tolerance
at
young
seedling
stage.
The
SNP
markers
associated
with
the
QTLs
identified
in
this
study
could
be
useful
for
further
marker-aided
breeding
aiming
at
developing
new
rice
cultivars
for
saline-prone
agro-ecosystems.
Keywords
Africa;
Hasawi;
Oryza
sativa;
RILs
;
SNPs;
Salt
tolerance;
Transgressive
segregation;
QTLs
Introduction
Grain
yield
of
rice
is
increasing
at
a
faster
rate
in
sub-Saharan Africa
than
the world’s
average;
between
2007
to
2012,
average
grain
rice
yields
in
sub-Saharan
Africa
increased
about
30%
or
108
kg.ha
-1
.year
-1
(AfricaRice,
2011),
Despite
this
grain
yield
increase,
rice
productivity
continues
to
be
affected
by
a
series
of
pests
blast,
bacterial
blight,
rice
yellow mottle
virus
and
stem
borers,
and
abiotic
factors
drought,
flood,
salinity,
cold
and
iron
toxicity,
in
this
continent.
Soil
salinity
in
reclaimed
paddy
fields
is
one
of
the
important
constraints
limiting
rice
growth
and
yield.
Salt-tolerant
cultivars
have
been
seldom
selected
in
Africa.
Furthermore,
there
are
not
many
advanced
salt-tolerant
breeding
lines
with
useful
agronomic
characteristics
due
to
the
difficulty
of
transferring
tolerant
traits
into
popular
rice
cultivars.
Likewise,
Munns
and
Tester
2008,
indicated
that
the
effect
of
salinity
is
caused
by
multigenic
traits
with
complex
genetics
and
mechanisms.
It
has
also
been
documented
that multi-genes
control
various
salt-tolerant
associated
traits
such
as
shoot
fresh
weight,
shoot
dry
weight,
shoot
length,
root
length,
and
shoot
Na+/K+
ratio
in
rice
(Akbar
et
al.,
1986;
Jones,
1986;
Yeo
and
Flowers,
1986;
Flowers
et
al.,
2000;
Ashraf,
2004;
Masood
et
al.,
2004;
Munns
and
Tester,
2008).
In
spite
of
this
difficulty,
efforts
have
been made
by
International Rice Research