Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 12

Applying Genomics Tools for
Molecular Studies and Breeding

(Xu et al. 2000), and the underlying genes were
finally cloned as a cluster of three ethylene-
responsive factor (ERF) genes, SUB1A , SUB1B ,
and SUB1C (Xu et al. 2006). It was demonstrated
through gene transformation that SUB1A was the
main contributor for tolerance (Xu et al. 2006);
and this finding has been confirmed through a
progeny test of recombinants identified within
the SUB1 cluster in several thousand individuals
in segregating populations (Septiningsih et al.
2009). It was also shown that SUB1A gene
expression, which subsequently determines the
amount of tolerance, is dosage-dependent. This
suggests that, for improvement in hybrid rice,
both parents should carry the SUB1A gene for
maximal effect (Septiningsih et al. 2009). In
addition, allelic survey studies showed that, in
some cases, the expression of SUB1A is a more
reliable parameter to use instead of the origi-
nal allelic determination, that is, the SUB1A-
1 -tolerant allele and SUB1A-2 -intolerant allele
(Singh et al. 2010; Septiningsih et al. 2012).

Identification of the QTLs and Genes
underlying Tolerance

Genetic dissection of quantitative traits using
QTL mapping tools became feasible with the
availability of DNA markers about two decades
ago. Even though varietal improvement can
be achieved using conventional breeding, QTL
mapping has tremendous potential to breed vari-
eties in a more effective and efficient way. Once
a major QTL for an important trait has been
mapped and the markers closely linked to the
locus have been identified, the QTL can be used
as a target in marker-assisted breeding to rapidly
breed an improved variety. Furthermore, once
the gene(s) underlying the QTL has(have) been
cloned, markers can be developed from the target
gene(s) for even more precise marker-assisted
breeding. The cloned gene(s) and near-isogenic
lines (NILs) that differ only at the locus of inter-
est also provide a starting point for detailed
study of molecular, physiological, and devel-
opmental mechanisms underlying the trait of
interest.

TolerancetoAnaerobicConditionsduring
Germination

Tolerance of flooding during seed germination,
referred to as anaerobic germination (AG), is
one of the most important traits necessary to
ensure good seedling establishment in direct-
seeded rice in both rain-fed flood-prone and irri-
gated ecosystems. Several QTLs for AG toler-
ance were reported on chromosomes 1, 2, 5, and
7 (Jiang et al. 2004, 2006). Our group at IRRI
identified several promising QTLs derived from
a tolerant donor from Myanmar, Khao Hlan On
(Angaji et al. 2010). The QTL with the largest
effect was detected on the long arm of chromo-
some9( qAG-9-2 or AG1 ), having a logarithm of
odds (LOD) score of 20.3 and explaining 33.5%
of the variation for this trait. Fine mapping of
this QTL in the background of IR64 narrowed
the locus down to a 58-kb region based on the
Nipponbare sequence. Several candidate genes
have been identified, and gene validation and

TolerancetoFlashFloodduringthe
VegetativeStage

FR13A was identified as one of the best
submergence-tolerant donors and was used
extensively by breeders in the 1970s; however,
very little was known about the genetic basis
of the tolerance possessed by this variety. Inde-
pendent studies using the submergence-tolerant
variety FR13A identified the major SUB1 QTL
and several minor QTLs (Xu and Mackill 1996;
Nandi et al. 1997; Toojinda et al. 2003). It was
found that SUB1 alone contributes 69% of the
phenotypic variance (Xu and Mackill 1996) and
could provide tolerance to complete submer-
gence for up to two weeks. SUB1 was then
fine-mapped to a region of 0.06 cM using an
F 2 segregating population of 2950 individuals