Biology Reference
In-Depth Information
Research Institute (IRRI) during the 1970s (Ver-
gara and Mazaredo 1975). Among other vari-
eties, FR13A, which was derived from pure-line
selection of the landrace “Dhalputtia” originat-
ing from Orissa, India, was identified as the
most tolerant cultivar (HilleRisLambers and Ver-
gara 1982) and subsequently used extensively
as a tolerant donor in breeding programs. Sev-
eral breeding lines tolerant of submergence have
been developed, including IR49830-7-1-2-1, a
highly tolerant and high-yielding indica-type line
(Mackill et al. 1993), which was released in
Cambodia under the name “Popoul” in 1999.
However, despite its tolerance of submergence,
this variety was not widely adopted by farm-
ers because it lacked several key traits, such
as locally preferred grain quality (Neeraja et al.
2007).
A major landmark in the history of
submergence-tolerance breeding was the iden-
tification of the major quantitative trait locus
(QTL)
Submergence 1
(
SUB1)
that controls this
trait (Xu and Mackill 1996). This early work
ultimately led to the cloning of the
SUB1
region
in FR13A and subsequently to the identifica-
tion of the ethylene-responsive factor (ERF)
gene
SUB1A-1
which is necessary and suffi-
cient for submergence tolerance (Xu et al. 2006).
Based on the sequence information,
SUB1
-
specific molecular markers were developed that
facilitated a precise marker-assisted backcross-
ing (MABC) system that is now successfully
being deployed to introgress the
SUB1
QTL
into widely grown “mega-varieties” in South and
Southeast Asia, as well as in Africa (Neeraja et al.
2007; Septiningsih et al. 2009; Bailey-Serres
et al. 2010; Manzanilla et al. 2011; Mackill
et al. 2012). As a result of repeated backcrossing
to the respective recipient parent, the improved
submergence-tolerant varieties carry the FR13A
SUB1
locus but are otherwise identical to the
original variety. Most importantly, grain quality
and other locally preferred traits are unaltered in
these new varieties, which enhance adoption by
farmers and variety release in the target coun-
tries. These new varieties are called “Sub1” or
“Scuba” rice.
Breeding direct-seeded rice varieties, which
requires tolerance of flooding during germina-
tion, also began in the past. However, success
was very limited mainly due to the lack of
tolerant donor varieties, and the complexity of
the trait (Yamauchi et al. 1993; Yamauchi and
Winn 1996; Biswas and Yamauchi 1997). More
recently, after screening thousands of rice acces-
sions, several landraces have been identified that
are tolerant of submergence during germina-
tion (also referred to as anaerobic germination,
AG) (Angaji et al. 2010). The analysis of map-
ping populations derived from tolerant donor
parents has led to the identification of promis-
ing QTLs that might be useful for direct-seeded
systems, as described in more detail below. As
was the case for submergence and AG tolerance,
efforts to develop varieties for stagnant flood-
ing and deepwater conditions were made over
several decades at IRRI (HilleRisLambers and
Seshu 1982). More recently, a concerted effort
has started to combine tolerance of stagnant
flooding with submergence tolerance (based on
SUB1
). This is particularly important for short
rice varieties, for example, Swarna, which was
the first mega-variety introgressed with
SUB1
(Swarna-Sub1). One variety that combines toler-
ance of submergence and stagnant flooding has
been developed by conventional breeding based
on phenotype selection (IRRI 119), which was
released in the Philippines as PSB Rc68 (Sep-
tiningsih et al. 2009; Mackill et al. 2010). More
recently, breeding lines that are high yielding and
perform well under stagnant flooding have also
been developed through conventional breeding
(Mackill et al. 2010).
This chapter will review the progress made in
applying genomics tools to unravel the molec-
ular and physiological basis of different types
of submergence tolerance, as well as efforts
to use this information to develop improved
rice varieties to meet the challenges of the
future.
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