Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 18

(a) (b)

S UB1 B

S UB1 C

SUB1A

S UB 1B

SU B1A - 2 S UB1 C

SU B1A - 1 S UB 1B S UB1 C

SUB1A-1
SUB1A-2

∗

(c) (d)

+Sub1

Submergence

Ethylene

ROS-scavenging
Recovery growth

-Sub1

SUB1A-1

Cell elongation
CHO consumption
Chl degradation

SLR1, SLRL1

Leaf elongation
CHO consumption
Chl degradation
Cell death

GA response

Fig. 2.3. SUB1 -specific markers and the molecular basis of submergence tolerance. The SUB1 locus contains either
two ( SUB1B , SUB1C )orthree( SUB1A , SUB1B , SUB1C ) ERF genes ( a ). Two different indica-/aus-specific SUB1A alleles
are known, of which the SUB1A-1 allele is present in submergence-tolerant varieties. Molecular markers distinguish
between varieties with and without SUB1A ( b , top panel) and between the SUB1A-1 and SUB1A-2 allele ( b , bottom
panel). The visible effect of the SUB1 locus is the suppression of growth during submergence and plant recovery within
about 2 weeks after de-submergence ( c ). Under submergence, ethylene induces the gibberellic acid (GA)-dependent
escape response, which is suppressed by SUB1A-1 -mediated maintenance of GA repression via the GA repressor proteins
SLR1 and SLRL1 ( d ). ROS, reactive oxygen species; CHO, carbohydrate, CHL, chlorophyll, GA, gibberellic acid, SLR1,
SLENDER RICE 1, SLRL1, SLENDER RICE LIKE 1. For a color version of this figure, please refer to the color plate.

SUB1A-1 is also the allele present in the SUB1
donor variety FR13A and FR13A-derived lines
that are now being used in Sub1 breeding pro-
grams (see above). The molecular markers used
for Sub1 breeding enable breeders to distinguish
between plants with and without the SUB1A
gene, and to discriminate between the alleles of
SUB1A (Figure 2.3b).
It has recently been suggested that the
SUB1A-2 allele can also confer tolerance of sub-
mergence since high expression of the SUB1A-
2 allele was observed in some varieties with
intermediate tolerance (Singh et al. 2010; Sep-

tiningsih et al. 2012). However, the most tol-
erant SUB1A-2 variety (James Wee) had a
submergence-survival rate of 44%, which is sig-
nificantly lower than SUB1A-1 varieties (51-
65%) (Singh et al. 2010). It remains to be
shown whether the higher tolerance mediated
by SUB1A-1 compared with SUB1A- 2 is related
to the level of transcription or post-translational
modification, for example, phosphorylation at
the putative MAP-kinase target site that is spe-
cific to the SUB1A-1 allele (Xu et al. 2006).
The main effect of SUB1A-1 is the sup-
pression of the “escape” response, which, in