Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 17

tolerance of complete submergence in rice (Ella
et al. 2003; Das et al. 2005; Sarkar et al. 2006).
Recovery after submergence was also faster in
the tolerant lines, resulting in greater production
of early tillers that subsequently produced pani-
cles, unlike the later tillers produced by the sen-
sitive lines, which mostly remained vegetative
through maturity. Consequently, the yield of the
tolerant lines was consistently and considerably
higher than that of the sensitive parents, ranging
from 1 t ha − 1 to over 3.5 t ha − 1 yield enhance-
ment over sensitive lines under field conditions
(Sarkar et al. 2009; Singh et al. 2009). All grain
quality aspects of the Sub1 lines were also either
similar to or better than those of the recurrent par-
ents after submergence. In addition, Sub1 intro-
gression lines also suffer less delay in flower-
ing and maturity than their parental lines (Singh
et al. 2009, 2011). Together, these data provided
sufficient evidence that the SUB1 gene can effec-
tively provide protection against flash floods and
can work across many genetic backgrounds and
environments. These conclusions were further
confirmed after additional Sub1 pairs became
available.

was similar. However, in areas that experienced
incidences of flooding, Sub1 varieties always
had higher yields, exceeding twice the yield of
the non-Sub1 types and checks in some cases,
particularly when the stress was severe. For
example, in one of the first set of trials con-
ducted with these lines in 2007, Swarna and
Swarna-Sub1 were compared at 32 sites in Uttar
Pradesh, India. Yields of the two varieties were
the same at sites that did not experience submer-
gence (averaging 5.5 t ha − 1 ). However, at most of
the sites, submergence of more than 5 days was
experienced, and the average yield of Swarna-
Sub1 was 3.67 t ha − 1 compared with 2.34 t ha − 1
for Swarna. Under more severe flooding of 15
days, the yield of Swarna-Sub1 was more than
double that of Swarna (2.7 t ha − 1 vs. 1.3 t ha − 1 ;
Mackill et al. 2012). This trend was consistently
experienced in subsequent trials conducted over
hundreds of sites in Asia every year. In almost
all trials, genotypes carrying SUB1 had higher
survival, with yield advantages of 1 3tha − 1

over the sensitive NILs based on the duration of
the flood and conditions of the floodwater.

−

Molecular and Physiological
Mechanisms underlying Tolerance

Sub1PerformanceinFarmers'Fields

A participatory approach involving farmers was
used to extensively evaluate the new Sub1 vari-
eties in South and Southeast Asia. This approach
provides information on the adaptation of these
varieties to local conditions and their reaction
to common pests and diseases, and also provides
direct feedback from farmers on their acceptance
of these varieties based on their local prefer-
ences. The data generated through these trials
are being used as part of the variety release pro-
cess in some countries, which also speeds up the
notification and commercialization of the new
varieties (Manzanilla et al. 2011; Paris et al.
2011). In most of these trials, comparisons were
made between Sub1 NILs and usually involv-
ing one or more varieties common among local
farmers as checks. At sites where there was no
flooding during the season, yield of both varieties

Tolerance of Transient Flooding during
the Vegetative Stage: The SUB1Mode
of Action

As mentioned above, the SUB1 locus contains
a variable number of ERF genes. In all ana-
lyzed japonica rice varieties, including Nippon-
bare, and in some intolerant indica varieties,
two ERF genes ( SUB1B , SUB1C ) are present
in the SUB1 locus (Figure 2.3a). The third gene,
SUB1A , is present only in submergence-tolerant
aus - and indica rice varieties, and in some intol-
erant indica varieties (Xu et al. 2006; Singh
et al. 2010). Two different alleles of the SUB1A
gene have been identified ( SUB1A-1 , SUB1A-
2 ) and the SUB1A-1 allele has been shown to
be the major determinant of submergence toler-
ance (Septiningsih et al. 2009; Xu et al. 2006).