Biology Reference
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sequencing (Yu et al. 2011; Thomson et al. 2011;
Elshire et al. 2011), are fast evolving and already
facilitate rapid and high-throughput genotyping.
Field screening experiments conducted with
bi-parental or association mapping populations
should ideally be conducted in target environ-
ments. If the genetic material screened is of
rather different plant type, as one typically
observes in association panels used in GWAS,
screening for grain yield alone would be poten-
tially misleading, since traditional rice genotypes
may be very tolerant but typically have low yield
potential and low harvest index. It may there-
fore be more advisable to screen for compo-
nent traits that contribute to P efficiency, such
as P-acquisition efficiency (PAE) or internal P-
utilization efficiency (PUE). In contrast to evalu-
ations of PAE that ultimately need to be done in
soil, Rose and colleagues (2011) established that
screening under such realistic soil/field condi-
tions would make the detection of genotypic dif-
ferences in PUE nearly impossible because any
difference in P uptake between genotypes would
confound measurements of PUE. It is therefore
crucial to evaluate PUE in a setup that guaran-
tees that genotypes have equal P content, and
the simple method developed by Rose and col-
leagues (2011) was designed to achieve that. One
additional P-efficiency trait that has been advo-
cated only recently is the development of cul-
tivars with reduced grain-P loading (Rose and
Wissuwa 2012). Currently, about 75% of the P
taken up by the rice crop is exported from the
field with the harvested grain (Rose et al. 2010).
Lowering grain-P concentrations to a level that
does not affect seedling vigor would therefore
offer opportunities to enhance long-term sus-
tainability of low-input systems by reducing P
mining, and sustainability of high-input systems
by reducing requirements for the application of
maintenance-P fertilizer.
The availability of large-effect genes/QTLs
and molecular markers facilitates pyramiding of
desirable alleles through MABC. Pyramiding of
submergence (
SUB1
) and salinity (
SalTol
) toler-
ance is already at an advanced stage and pyra-
miding of
Pup1
with major drought QTLs is in
preparation (IRRI unpublished data). For pyra-
miding, individual QTLs are first introgressed
into a widely grown and locally well-adapted
rice variety (mega-variety; e.g., IR64) and the
genetic makeup of the recipient parent is then
restored through MABC, that is, a series of two to
three backcrosses and marker-assisted selection
of progenies with the QTL and minimal presence
of markers for background donor segments. In a
second step, the individual introgression lines
(i.e., IR64-SUB1, IR64-SalTol, and IR64-Pup1)
are crossed and progenies selected using QTL-
specific foreground markers. Since the genetic
background of the individual QTL lines is nearly
identical, background genotyping can be reduced
to a minimum.
This principle, so far followed to combine
tolerance of multiple stresses, would be equally
suited for pyramiding tolerance components for
a given trait such as P efficiency. As outlined
above, the limiting factor is now a lack of
validated, large-effect QTLs/genes and efforts
should thus focus on identifying those. This
search for novel P-efficiency alleles would have
to be broadened beyond the current focus on
mechanisms improving P uptake, to include
QTLs/genes controlling internal P-utilization
efficiency and grain-P content. We believe this
to be crucially important because improvements
in either alone would not assure long-term sus-
tainability of cropping systems with regard to P.
In fact, the very recent paradigm shift in
dissecting natural variation in crops such as
rice away from bi-parental populations with
their limited variability to SNP-based or even
sequence-based association mapping of pan-
els consisting of gene bank accessions for the
first time makes it possible to tap the variation
present in gene pools hidden in gene-bank col-
lections. Advances in genotyping technologies
are beginning to remove most limitations with
regard to genotypic characterizations, for both
exploratory and breeding purposes. Decreasing
costs per marker or data point and the possibility
of outsourcing marker analysis to service labs
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