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Molecular Plant Breeding Provisional publishing
Molecular Plant Breeding 2012, Vol.3, No.10, 103
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believe that the
SalTol
locus is located within the
region of the three markers RM8094, RM3412 and
RM493, as shown in Figure 2. This result was
consistent with our previous mapping experiments,
which found that RM8094 is the most tightly linked
marker of the
SalTol
QTL, with the highest LOD peak
(Islam et al., 2011b).
Seven haplotypes were identified among the 115
genotypes (Figure 1) when the marker alleles for the
best three SSR markers were used to compare
haplotypes using FL478 as a reference. The FL478
haplotype (haplotype 1) was found in five genotypes,
and this was very important for tracking
SalTol
with
molecular markers. Among the 115 genotypes, 76
genotypes had none of the same marker alleles as the
FL478 haplotype (haplotype 7).
Among the 12 popular BRRI-developed rice varieties,
all had haplotypes different from that of FL478.
Different marker alleles from FL478 or Pokkali
were produced for the marker RM8094 in the BRRI
varieties.
Considering the haplotypes for FL478, it was found
that the entries that had one of the FL478-type marker
alleles for locus RM8094 were found to be either
tolerant or moderately tolerant of salinity (Table 3). It
was found that lines PSBRc82, IR4630-22-2-5-1-5,
Pelita I-1, IR66404-4B-20-1-2, IR71866-3R-1-2-1,
IR65775-4B-19-1-3 and PSBRc50 had the FL478
marker allele for the RM8094 marker and all of these
lines/varieties were found to be tolerant to moderately
tolerant of salinity (score 3 and 5); none of them were
susceptible (Table 3). Therefore, marker RM8094
appears to be diagnostic of salinity tolerance. The 115
genotypes that had the same allele as FL478 for marker
RM3412 were found to have a mixed reaction to salinity
stress (Table 3). A similar result was also found for
marker locus RM493. Therefore, these two markers
(RM3412 and RM493) must not be used for MAS in
populations derived from these susceptible parents.
It was also found that some of the varieties, such as
Pokkali-2, Pokkali-4, Pokkali-6, Kalimekri, Cheriviruppu,
IR886-30-3-1-4-2, Bhirpala, CR1015, Kajalsail,
IR71907-3R-2-1-2, IR71897-3R-1-1-2, IR55182-3B-
14-3-2-3, IR58430-6B-14-1-2, IR63295-AC211-3,
IR64197-3B-8-2, IR74099-3R-2-2, IR71991-3R-2-1,
IR65192-4B-14-1, IR60483-2B-17-2-1-2, IR72048-B
-R-11-1-3-1-2B-2, IR58443-6B-10-3 and IR71991-3-
R-2-6-1, had no common FL478 marker alleles for
RM8094, RM3412 and RM493 (Table 3). However,
these lines were highly tolerant of salinity (score 3) at
EC 12 dS m
-1
. These results suggest that QTLs other
than
SalTol
control salinity tolerance in these tolerant
genotypes. Therefore, these genotypes may represent
novel sources of salinity tolerance, and could
potentially be exploited to identify new QTLs other
than
SalTol
.
For the seven different sources of Pokkali that were
tested, we found that all of them were different except
for Pokkali-5 and Pokkali-7. The most widely used
salt-tolerant line, FL478, was derived from the cross
between IR29 and Pokkali. However, the original
Pokkali accession used for making this cross was not
properly documented. So, in this study, we were trying
to identify which source of Pokkali contributed the
SalTol
region in FL478. Results showed that Pokkali-1
possessed the same marker alleles as FL478 in the
SalTol
region in FL478. Among the seven microsatellite
markers, all the markers produced the same SSR
marker alleles as FL478 except for RM140; this was
similar to the other parent, IR29 (Table 3 and Figure
2). This result suggested that the region containing the
locus RM140 was contributed by IR29 and other
segments containing the marker loci RM8094,
RM3412 and RM493 by Pokkali-1. Therefore, it was
suggested that, among the seven Pokkali sources,
Pokkali-1 contributed the
SalTol
region in FL478.
This result was contrary to the previous report of
Walia et al (2005), who reported that IR29 was the
source of the
SalTol
region in FL478.
The SSR markers linked to the
SalTol
QTL were
analyzed and showed that RM8094, RM3412 and
RM493 are useful markers for identifying genotypes
with salinity tolerance at the seedling stage. These
validated SSR markers can be used for marker-assisted
selection to introgress the
SalTol
QTL from a donor to
a recurrent genotype. The FL478 haplotype was found
in five genotypes, Pokkali-1, FL378, IR4630-22-2-5-