Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 23

popular varieties in the future. The introgression
of the major QTL AG2 derived from Ma-Zhan
Red into several popular varieties has also begun.
It is interesting to note that most of the major
QTLs controlling tolerance of flooding during
germination or anaerobic germination derived
from different tolerant donors identified so far
are located in different positions in the rice
genome (Angaji et al. 2010; Septiningsih et al.
2013; unpublished data). However, the contribu-
tion of each QTL to AG tolerance ranged from
small to medium. This suggests that, unlike the
case with the SUB1 gene, the introduction of
one QTL only into popular varieties or breeding
lines will not give the level of tolerance needed.
Assuming that their contributions are additive
and there are no yield and quality penalties, the
best strategy to increase the tolerance of AG
stress is QTL pyramiding. The active pipeline
of our research in discovering novel major QTLs
from diverse tolerance donors will give us more
opportunities in searching for the best com-
bination of multiple QTLs for different target
environments. Ultimately, these pyramided lines
could be used directly as improved varieties or
could be combined with tolerance of different
types of flooding or some other key traits for
direct-seeded environments or other abiotic and
biotic stresses according to the needs of the target
environments.

followed by reoxygenation allowed the identi-
fication of several genes that are strongly regu-
lated under AG stress (Narsai et al. 2009). How-
ever, these studies are just beginning to unravel
the complex mechanisms underlying tolerance
of AG. The genetic and molecular basis of tol-
erance of AG needs to be further investigated
so that advances in knowledge can be applied to
rice improvement. Tolerant donors identified at
IRRI provide an excellent opportunity to further
unravel the genetic and molecular basis of toler-
ance and to develop more resilient rice varieties
that can overcome some of the current obstacles
associated with rice cultivation.

Exploring the Genetic Control of
Tolerance of Stagnant Flooding

Despite the development of several IRRI vari-
eties and many elite breeding lines with tol-
erance of stagnant flooding, there is still a
complete lack of genetic information regard-
ing the control of stagnant flooding tolerance
and extremely limited information regarding the
physiology of this trait. Accordingly, elucidating
the genetic control of stagnant flooding tolerance
is a major objective of the breeding program.
Efforts are under way to exploit shortcut QTL-
mapping methods such as selective genotyping
and early-generation mapping populations (e.g.,
F 2 -derived bulks) in order to identify QTLs using
classical QTL-mapping approaches in a rela-
tively short time frame. A recombinant inbred
population is also being developed for map-
ping QTLs from the IRRI 154 source. Plans are
under way to evaluate a large range of elite and
adapted IRRI material. The International Rice
Germplasm Collection (IRGC) has also been
exploited for identifying novel sources of tol-
erance. The use of backcross-derived mapping
populations would be the most effective way to
integrate QTL mapping with the development of
new breeding material.
Alternatively, association-mapping appro-
aches could be used. Given that considerable
variation exists in elite breeding material of

UnravelingtheGeneticandMolecular
MechanismsunderlyingToleranceofFlooding
duringGermination

Tolerance of AG is independent of tolerance of
submergence during the vegetative stage, con-
ferred by the SUB1 QTL. In this case, the
donor for the SUB1 QTL, FR13A, is suscep-
tible to AG. It has been reported that CIPK15
[calcineurin B-like (CBL)-interacting protein
kinase] plays an important role in tolerance of
AG (Lee et al. 2009). Additionally, transcript
profiling of coleoptiles under anaerobic con-
ditions (Lasanthi-Kudahettige et al. 2007) and
germinating embryos under anoxia or anoxia