Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 26

rapid gains could be exploited in breeding using
these sources (in contrast to unadapted sources
such as landraces). Field evaluations across mul-
tiple sites and years for the latter two varieties
indicate a moderate tolerance presumably due to
the presence of minor or moderate-effect QTLs
that are probably unlinked to SUB1 .
Alternative QTL detection methods such as
“marker-evaluated selection” (Steele et al. 2004),
which are based on the principle of genotyping
selected breeding material to identify genomic
regions under selection, could also be useful
for preliminary mapping of QTLs associated
with this trait, because submergence is usu-
ally screened in the F 2 and F 3 generations.
Germplasm evaluations have been undertaken
to identify potentially new sources by pheno-
typic and genotypic screening of germplasm to
identify novel sources of tolerance that could
potentially be combined with SUB1 (Singh et al.
2010).

areas where floodwaters are often saline. A major
QTL called Saltol has been identified on chro-
mosome 1 and has been characterized recently
(Thomson et al. 2010). However, multiple QTLs
are probably required to achieve sufficient salin-
ity tolerance in the field (G. Gregorio, IRRI,
pers. comm.) and additional QTLs for seedling-
and reproductive-stage salinity tolerance may be
needed to provide protection from salinity stress
throughout the season.
The opportunity to apply molecular marker
technologies as a means of combining multi-
ple tolerance genes/QTLs into individual rice
varieties provides an unprecedented opportunity
for breeders to rapidly develop tolerant cultivars
for targeted environments. However, today the
number of large-effect QTLs is still small and
many reported QTLs are not sufficiently char-
acterized, that is, data on the effect of QTLs
in different genetic backgrounds and environ-
ments are not available. Without this informa-
tion, it will be difficult for breeders to use
QTLs in their breeding programs. With the rapid
progress made in genome sequencing technolo-
gies and high-throughput marker technologies,
it can be expected that more large-effect QTLs
will be identified in the future. This will be even
more important in light of climatic changes that
adversely affect rice production, especially in
rain-fed lowland ecosystems.

PyramidingofSUB1withOtherAbioticand
BioticStress-toleranceTraits

The identification of major tolerance genes and
QTLs for important abiotic (e.g., drought, salin-
ity, phosphorus deficiency) and biotic stresses
will permit the use of marker-assisted pyramid-
ing to combine multiple genes/QTLs in individ-
ual rice varieties. Bacterial blight and other dis-
eases are prevalent in flood-prone regions and are
exacerbated by flooding (Nino-Liu et al. 2006).
As major genes for disease resistance have been
identified, this provides opportunities for pyra-
miding bacterial blight, blast, and virus resis-
tance with SUB1 .
Rain-fed rice areas exposed to regular flash
floods and stagnant flooding can also experi-
ence periods of low rainfall causing drought
stress. Large-effect QTLs that confer tolerance of
drought at the reproductive stage have been iden-
tified (Bernier et al. 2007; Vikram et al. 2011)
and are available for pyramiding with SUB1 .
The pyramiding of submergence and salinity tol-
erance is also important, especially for coastal

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