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Molecular Plant Breeding Provisional publishing
Molecular Plant Breeding 2012, Vol.3, No.10, 103
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104
the trait, it has been difficult to develop an accurate,
rapid and reliable screening technique. Molecular
markers are widely accepted as potentially valuable
tools for crop improvement of rice (Mackill et al.,
1999; McCouch and Doerge, 1995). Molecular
markers will play a vital role in enhancing global
food production by improving the efficiency of
conventional plant breeding programs (Collard and
Mackill, 2008). The progress and technical advances
in molecular marker technology facilitate the
identification of the major genes/QTLs for biotic and
abiotic stresses in rice. The development of molecular
marker selection permits the rapid and accurate
identification of individuals that contain genes for
salt tolerance.
DNA-based markers can be used to assess genetic
diversity across an entire genome or specific
chromosome regions. Bai et al (2003) and Liu and
Anderson (2003) used microsatellite markers associated
with a major QTL on chromosome 3BS for Fusarium
head blight resistance identified in Sumai 3 to identify
lines that putatively carry the 3BS QTL. To determine
the suitability of identified markers linked to a QTL,
SSR haplotyping was used, which has recently been
used in rice. Diverse genotypes were selected to
determine the level of polymorphism of SSR
markers and to compare the haplotypes of tolerant
or resistant genotypes.
An experiment with quantitative trait loci (QTL) for
salt tolerance in rice was conducted using amplified
fragment length polymorphism (AFLP), restriction
fragment length polymorphism (RFLP) and
microsatellite markers in different populations
(Gregorio, 1997; Lang et al., 2000; Tuan et al., 2000;
Bonilla et al., 2002; Niones, 2004; Thomson et al.,
2010; Islam et al., 2011(a)). Microsatellite markers
have been effective in mapping QTLs associated with
salt tolerance (Lang et al., 2001). A major QTL for salt
tolerance was mapped on chromosome 1 by using an
F
8
recombinant inbred line (RIL) of a Pokkali/IR29
cross (Gregorio, 1997). This QTL on chromosome 1
controlled the Na-K absorption ratio and accounted
for 64.3 to 80.2% of the phenotypic variation in salt
tolerance with LOD>14.5. This chromosome 1
segment was further saturated using RFLP and SSR
markers using the RIL (Bonilla et al., 2002). The
identified Na
+
, K
+
and Na-K absorption ratio QTLs
accounted for 39.2, 43.9 and 43.2% of the phenotypic
variation with LOD>6.7. This segment of chromosome 1
was further fine mapped by using near isogenic lines
(NILs) of the backcross of Pokkali/IR29 (Niones,
2004) with microsatellite markers. Pokkali has been
the most widely used salt-tolerant parent by rice
breeders. A newly developed elite line, FL478, from
the cross of IR29 and Pokkali became popular as a
novel source of salinity tolerance at seedling stage,
because it possessed higher salinity tolerance than
Pokkali and possessed many desirable traits.
The objectives of this study were to (i) compare the
SSR marker haplotypes of salinity-tolerant genotypes
with those of FL478 and Pokkali at the known
SalTol
QTL on chromosome 1; (ii) identify salinity-tolerant
rice varieties/lines with putatively novel salinity
tolerance sources; and (iii) identify the contributor of
the
SalTol
region on chromosome 1 in FL478.
1 Results
The seedling stage salinity tolerance evaluation
demonstrated that 37 genotypes were rated as tolerant
to highly tolerant (score 1 and 3), 42 were moderately
tolerant (score 5) and 36 were susceptible (score 7 and
9) (Table 1 and Table 3).
Among the seven
SalTol
linked markers, the highest
number of alleles was found in RM8094 (15),
followed by RM1287, RM3412 and RM493 (10),
RM140 (8), CP03970 (5) and CP6224 (3), which
produced the lowest number of alleles, and the
average was 8.71 (Table 2). The PIC values ranged
from 0.54 to 0.89, with an average of 0.75. The
highest PIC value (0.89) was found for the RM8094
locus followed by RM493 and RM3412 (0.81) and
RM1287 and RM140 (0.77).