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kinase ( OsPupK46-2 ) (Chin et al. 2011). The
predicted gene models of the dirigent gene and
the protein kinase were subsequently revised
based on detailed sequence comparisons with
other members of the dirigent and protein kinase
gene families, as well as by cDNA sequencing.
The revised gene models are available under
accession number BAK26565 and BAK26566,
respectively. OsPupK46-2 encodes a functional
Ser/Thr protein kinase and was recently re-
named PHOSPHORUS STARVATION TOLER-
ANCE 1 ( OsPSTOL1 ; Gamuyao et al. 2012)
after it was shown that this gene is the major
determinant of tolerance. Analyses of transgenic
plants with constitutive OsPSTOL1 expression
(35S:: OsPSTOL1 ) showed that OsPSTOL1 acts
as an enhancer of crown root growth at an early
developmental stage. This increases the root sur-
face area and enables plants to forage a larger
soil area and to take up more P and other nutri-
ents (Gamuyao et al. 2012). It was further shown
that the OsPSTOL1 promoter was active in the
coleoptilar node, specifically in the parenchy-
matic cell layer and in primordia of crown
roots, which constitute the post-germination
root system in rice. Gene expression profiling
using an Affymetrix array further showed that
root growth-related and stress-responsive genes
were differentially expressed in 35S:: OsPSTOL1
overexpression plants (Gamuyao et al. 2012),
whereas P-starvation genes were not differen-
tially expressed in agreement with earlier data
derived from Nipponbare- Pup1 NILs (Pariasca-
Tanaka et al. 2009).
Importantly, OsPSTOL1 is located within the
Kasalath-specific INDEL region and is therefore
absent from the Nipponbare reference genome.
The same was found for the major QTL SUB-
MERGENCE 1 ( SUB1 ), which confers toler-
ance of complete submergence for up to two
weeks (for review, see Septiningsih et al. 2013).
In Nipponbare, the SUB1 locus contains two
ethylene-responsive transcription factor genes
( SUB1B and SUB1C ), whereas an additional
gene ( SUB1A ) is present in the tolerant SUB1
locus, which was shown to be the major deter-
minant of tolerance (Xu et al. 2006). The SUB1
and Pup1 QTLs thereby exemplify possible lim-
itations of reverse genetic approaches, since they
show that tolerant genotypes might possess novel
genes and/or employ mechanisms and pathways
that are distinct from stress responses in the
model variety Nipponbare, which is intolerant.
Pup1-specific Molecular Markers
The identification of major tolerance genes in
QTLs is of value for breeding since highly spe-
cific markers can be developed. However, know-
ing the specific gene is not a prerequisite for
breeding as long as closely flanking markers are
available. More important for breeding appli-
cations is that the effect of a given QTL is
determined in different environments and genetic
backgrounds. Since this requires several gen-
erations of crossings and screening in at least
two sites and seasons, considerable resources are
needed. Most published QTLs are therefore not
advanced to this level and this is the main rea-
son why, despite the large number of reported
QTLs, only a very few are actively used in breed-
ing programs (Xu and Crouch 2008). However,
some major QTLs are already used for molecular
breeding of tolerant rice varieties. This includes
the SUB1 QTL (Xu et al. 2006; Septiningsih
et al. 2009), the salinity tolerance QTLs SalTol
and qSKC1 (Thomson et al. 2010; Ren et al.
2005), as well as QTLs for anaerobic germina-
tion (Angaji et al. 2010) and drought tolerance
(Kumar et al. 2007; Bernier et al. 2009a; Bernier
et al. 2009b; Vikram et al. 2011). Submergence-
tolerant rice varieties with the SUB1 QTL have
been quickly adopted by farmers and already
show a large impact in flood-prone environments
in Asia (Mackill et al. 2012; Manzanilla et al.
2011).
The Sub1 rice varieties have been developed
by a marker-assisted backcrossing (MABC)
approach, which facilitates targeted and precise
introgression of a target QTL. In contrast to
other approaches, MABC uses locally adapted
and widely grown rice varieties as the QTL
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