Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 13

characterization are under way (unpublished
data). This QTL is a promising target for marker-
assisted selection for direct-seeded rice varieties.
Another major QTL was detected on the short
arm of chromosome 7 (referred to as qAG7.1
or AG2 ), derived from the tolerant donor vari-
ety Ma-Zhan Red (Septiningsih et al. 2013).
NIL development for fine mapping and vari-
etal improvement for this QTL are under way.
This QTL can be combined with AG1 to confer
higher tolerance, given that the effect of the two
QTLs proved to be additive or synergistic. Stud-
ies using other unrelated sources of tolerance are
under way to identify additional QTLs involving
different tolerance mechanisms.

gence, phosphorus deficiency, and deep water
(Xu et al. 2006; Hattori et al. 2009; Heuer et al.
2009).

Development of Sub1 Varieties

Identification of the SUB1 gene enabled marker-
assisted selection (MAS) for submergence toler-
ance. The SUB1 QTL has a large effect and the
phenotypic difference between tolerant and sus-
ceptible types is consistent. A wealth of sequence
polymorphisms in and around the gene cluster
from both tolerant and susceptible parents pro-
vided useful markers for MAS (Xu et al. 2006;
Neeraja et al. 2007; Septiningsih et al. 2009;
Singh et al. 2010; Iftekharuddaula et al. 2011).
Given the popularity of high-yielding varieties
with grain quality attributes that lacked sub-
mergence tolerance, a large-scale MABC pro-
gram was undertaken at IRRI using these pop-
ular varieties as recurrent parents. Instead of
using the original donor FR13A, two FR13A-
derived improved lines were used as donors:
IR49830-7-1-2-2 (IR49830-7) and IR40931-33-
1-3-2 (IR40931-33) (Mackill et al. 1993). This
led to successful introgression of the SUB1 locus
into several popular varieties (mega-varieties)
in India, Bangladesh, Indonesia, Laos, and the
Philippines. By using precision MABC, the high
yield and desirable grain and eating qualities of
these mega-varieties were retained (Septiningsih
et al. 2009; Singh et al. 2009).
Three levels of MABC were applied to ensure
high precision in breeding and to reduce the
time required for variety development: (1) fore-
ground selection, in which markers tightly linked
to SUB1 are used to select for the locus; (2)
recombinant selection, in which closely linked
flanking markers are used to minimize the
donor chromosomal segment containing SUB1 ;
and (3) background selection, in which DNA
markers are used to accelerate the recovery of
the recurrent parent genome (Figure 2.1; Col-
lard and Mackill 2008). The method of select-
ing recombinants on both sides of the target

DeepwaterRice

The most important trait for the survival of deep-
water rice is rapid underwater internode elonga-
tion, to ensure that upper leaves maintain effi-
cient photosynthesis (Catling 1992; Vergara et al.
1976). A number of studies have identified QTLs
for deepwater traits, such as internode elongation
and number of elongated internodes (Sripong-
pangkul et al. 2000; Nemoto et al. 2004; Hattori
et al. 2007; Kawano et al. 2008). Even though dif-
ferent donors were used in studies on deepwater
rice, QTLs on chromosomes 1, 3, and 12 were
repeatedly detected in different mapping pop-
ulations. Through NIL evaluation, it was con-
firmed that the QTL on chromosome 12 con-
tributed the most rapid internode elongation in
deepwater stress conditions (Hattori et al. 2008).
By positional cloning, Hattori and colleagues
(2009) identified the genes within this QTL:
SNORKEL1 ( SK1 ) and SNORKEL2 ( SK2 ). Like
the SUB1 s, these are ERF genes of subgroup VII,
possessing a single AP2 DNA-binding domain.
Both SK1 and SK2 are missing in the elite recur-
rent parent genome (Hattori et al. 2009). The
presence of genes conferring abiotic stress toler-
ance have recently been found in donor landraces
but not in the reference Nipponbare genome, as
in the case of the donors for tolerance of submer-