Applying Genomics Tools for Breeding Submergence Tolerance in Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 14

Background selection for MABC

RM23668 (0.6 Mb)
RM23679 (0.8)
RM316 (1.0)

RM23778 (3.9 Mb)

0 Mb

RM23788 (4.2)

RM8303 (2.3)

Centromere (2.7 Mb)

RM23805 (4.5)

RM23770 (3.7)
RM23772 (3.8)
RM23778 (3.9)
RM23788 (4.2)
RM23805 (4.5)

RM5899 (5.1)

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10.4 Mb

RM23831, RM23833 (5.4)

Sub1 region

RM23835 (5.5)

RM464 (6.5)
RM23887 (6.5)
RM23917 (7.3)
RM23922 (7.4)
RM23928 (7.5)
RM219 (7.8)
RM23958,
RM23957 (7.9)

Recombinant
markers

RM444, RM23852 (5.9)

RM23865 (6.2)
RM23869 (6.3)
Sub1

Sub1C173
ART5
GnS2
AEX1

Foreground
markers

RM464 (6.5)
SC9/RM23887 (6.5)

RM24005 (9.2)
RM24011 (9.3)

SC3/RM8300 (6.6)

RM24046 (10.1)
RM24070 (10.4)

Recombinant
markers

RM6920 (7.0)

22.6 Mb

RM23911 (7.1)

RM23915, RM23916 (7.2)

RM23917 (7.3)

Fig. 2.1. Marker-assisted backcrossing (MABC) for SUB1 . A number of markers have been identified as useful
foreground markers (used to retain the tolerant SUB1 allele) and recombinant markers (flanking markers used to select for
a small SUB1 introgression). Once foreground and recombinant selection have reduced the population size, background
selection is performed to eliminate donor introgressions across the rest of the genome and return to the recurrent parent
genome (see inset). For a color version of this figure, please refer to the color plate.

locus in at least two backcross (BC) genera-
tions during MABC was first proposed by Young
and Tanksley (1989) and applied in rice by
Chen and colleagues (2000). Foreground and
recombinant polymerase chain reaction (PCR)-
based DNA markers, such as simple sequence
repeat (SSR), cleaved amplified polymorphic
sequences (CAPS), insertion/deletion (INDEL),
and mismatched single nucleotide polymor-
phism (SNP) markers were generated to facil-
itate introgression of the SUB1 allele from the
FR13A-derived lines in the background of popu-
lar varieties through MABC (Neeraja et al. 2007;
Septiningsih et al. 2009). The most common
markers used for foreground selection are sum-
marized in Table 2.1.
In the first stage, six varieties were enhanced
with SUB1 using MABC (Neeraja et al. 2007;

Septiningsih et al. 2009; Iftekharuddaula et al.
2011). In 2011, with the addition of Ciherang-
Sub1 and PSB Rc18-Sub1, a total of eight
Sub1 mega-varieties have now been developed
(Table 2.2; Figure 2.2). Evaluation of these new
cultivars has indicated that there is no negative
effect of SUB1 on other traits, and no linkage
drag, especially as recombinant selection was
performed. In many cases, the development of
these new Sub1 varieties will make it easier to
incorporate SUB1 in the future because recom-
binant and background selection may not need
to be as rigorous because the donor parents
are highly adapted and possess many desirable
agronomic characters. For example, a single
backcross has been used for the development of
Ciherang-Sub1 using IR64-Sub1 as the donor
parent; this donor is closely related to the