Biology Reference
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in themselves are either beneficial or have no
inhibitory effects on metabolism. Examples are
soluble sugars, free amino acids such as proline,
and K + ions. The first two are synthesized organ-
ically, and thus up-regulation of the enzyme
systems that produce them is known to confer
tolerance. However, synthesis obviously incurs
a significant metabolic cost and, in addition, the
accumulation of organic compounds does not
inherently prevent the accumulation of Na + to
toxic concentrations. These “compatible solutes”
are probably more important when the harmful
ions such as Na + are effectively compartmented
in the vacuoles, with the buildup of these solutes
in the cytoplasm preventing internal dehydra-
tion, and consequently decreasing the osmotic
potential of the root tissue to facilitate water and
nutrient uptake (Ismail et al. 2007).
Third, high NaCl concentrations also result in
high Cl levels. The effect of Cl is somewhat
controversial. In many species, it is believed to
have a significant toxic effect, whereas, in oth-
ers, such as rice, it may not exert harmful effects
or might even contribute to osmotic adjustment
(Garthwaite et al. 2005; Diedhiou and Golldack
2006; Teakle et al. 2007; Brumos et al. 2009;
Tavakkoli et al. 2010, 2011). Fourth, high salin-
ity also causes a wide range of secondary effects.
For example, high Na + in solution interferes
with the solubility of other metal ions such as
Ca 2 + and many micronutrients. This can result
in deficiencies, which can exacerbate the toxic
effects of Na + and, in some situations, the toxic
effects may partially result from these deficien-
cies. Application of exogenous Ca 2 + is well
known to reduce the severity of Na + stress (Tobe
et al. 2003; An et al. 2004; Shabala et al. 2006;
Zhang et al. 2011).
Another general consequence of salinity
stress (whether ion toxicity, osmotic stress, or
nutrients stress) is the effect on metabolism. Pho-
tosynthesis is adversely affected, through both
stomatal closure and direct effects on the pho-
tosynthetic machinery (Yeo et al. 1985; Khan
et al. 1997; Moradi and Ismail 2007). A sig-
nificant increase in the concentrations of reac-
tive oxygen species (ROS, i.e., hydrogen per-
oxide, hydroxyl radicals, and the like), which
are highly toxic, was frequently reported as the
consequence of salt stress (Moradi and Ismail
2007; Yamane et al. 2009; Ghosh et al. 2011).
Many pathways exist for detoxification of ROS
and up-regulation of these pathways often raises
tolerance of salinity stress (Badawi et al. 2004;
Sunkar et al. 2006; Moradi and Ismail, 2007; Hou
et al. 2009; Lu et al. 2011). ROS are also required
for cell expansion and as signaling molecules
in various responses, and up-regulation of these
pathways can sometimes lead to growth inhi-
bition (Rodriguez et al. 2004; Taleisnik et al.
2009; Bernstein et al. 2010). Finally, Na + stress
is directly sensed by the plant and can induce var-
ious hormonal and growth responses (Zhu 2003),
though these sensing mechanisms and the sen-
sors/receptors are still not known.
Mapping of Loci Associated with
Salinity Tolerance inRice
Over the past 15 years, numerous QTL studies
have investigated the genetic basis for salinity
tolerance in rice in a number of donors, resulting
in the identification of many genetic loci control-
ling various physiological mechanisms related
to tolerance. The most widely reported - though
by no means the first - QTL study is that of
Lin et al. (2004). They studied an F 2 population
derived from a cross between the highly toler-
ant Indian indica landrace Nona Bokra and the
highly sensitive japonica variety Koshihikari. A
total of 11 QTLs from six non-overlapping loci
were identified controlling root and shoot Na +
and K + traits, and survival, and one QTL was
subsequently fine-mapped and identified as the
OsHKT1.5 gene (Ren et al. 2005).
Comparisons of these results with other
previously and subsequently published studies
(Prasad et al. 2000; Gong et al. 2001; Bonilla
et al. 2002; Takehisa et al. 2004; Ismail et al.
2007; Lee et al. 2007; Zang et al. 2008; Sabouri
et al. 2009; Thomson et al. 2010; Alam et al.
2011) and our recent unpublished studies show
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