Molecular Breeding for Phosphorus-efficient Rice - Translational Genomics for Crop Breeding: Abiotic Stress, Yield and Quality - page 76

Recipient Donor F 1 F 2 selected F 2 BC 2 F 1 BC 2 F 4 NIL*

selfing

BC

selection selfing

Pup1

Background 100%
introgression
(SSR and SNP markers)

~ 50%

~14% ~7%

IR64 IR64- Pup1

BC 2 F 4

Kasalath

( Pup1 donor)

Fig. 5.4. Marker-assisted breeding of Pup1 varieties. The tolerant rice variety Kasalath (photo at the left) or Nipponbare-
Pup1 lines were used as donors for the Pup1 QTL located on chromosome 12 (shown as red bars; Pup1 QTL indicated in
blue). After crossing with an intolerant recipient variety without Pup1 (Chr. 12 indicated as white bars), F 1 progenies and
the following backcross (BC) and selfing generations are selected using Pup1 foreground markers (blue arrows), flanking
markers (purple arrows), and background markers (red arrows). Representative IR64- Pup1 plants at the BC 2 F 4 generation
are shown in the photo to the right. Remaining donor introgression in the different generations was determined using SNP
markers and indicated as percentage (all chromosomes). *The introgressions in the schemes do represent the actual data;
NILs without any remaining background introgressions are hypothetical and probably not attainable. For a color version of
this figure, please refer to the color plate.

used (Thomson et al. 2011). In the case of IR64-
Pup1 , the SNP data showed about 14% remain-
ing donor segments in selected BC 2 F 1 plants
and about 7% in BC 2 F 4 (Figure 5.4). To further
restore the genome of the recipient parent, con-
tinuous selection under stress and control con-
ditions and additional backcrosses are required.
However, with increasing marker density, it
can be expected that small remaining donor
introgressions will be detected even in later
generations.
The availability of molecular markers
revealed that, of the varieties that were selected
as Pup1 -recipient parents, only IR64, IR74, and
Situ Bagendit did not naturally possess Pup1 .In
contrast, the tolerant allele for OsPSTOL1 was
detected in Batur and Dodokan (Figure 5.5b;
Chin et al. 2011). In agreement with this, data
derived from a field experiment in Indonesia
showed that a beneficial effect of Pup1 under
low-P conditions was indeed observed only in
Situ Bagendit- Pup1 breeding lines (Chin et al.
2011). The natural presence of the OsPSTOL1
gene in Batur and Dodokan, which are supe-
rior Indonesian upland varieties, is not surpris-
ing since earlier data had already shown a high
degree of Pup1 conservation in drought-tolerant
rice (Heuer et al. 2009; Chin et al. 2010; Chin
et al. 2011). In contrast, the Pup1 locus is absent

from most irrigated rice varieties and it was
unclear whether Pup1 would show any effect
in irrigated rice systems. It is therefore encour-
aging that data derived from P-deficient irrigated
field experiments showed enhanced early vegeta-
tive growth of IR74- Pup1 breeding lines (Figure
5.5c), as well as enhanced grain yield compared
with IR74 and sister lines without Pup1 (Fig-
ure 5.5c, d; Chin et al. 2011). However, under
these conditions, Pup1 does not appear to have
an effect in the genetic background of IR64 (Fig-
ure 5.4d) and additional field screenings under
rain-fed/drought conditions are now ongoing to
further evaluate IR64- Pup1 and to draw final
conclusions. Overall, the field data derived from
Situ Bagendit- Pup1 and IR74- Pup1 suggest that
Pup1 has the potential to confer yield advantages
of 10-50% under low-P conditions, depending
on the genotype and experimental conditions
(Chin et al. 2011; Heuer et al. unpublished).

Phenotyping for Low-P Tolerance

Screening for tolerance of P deficiency under
field conditions is constrained by the fact that
the distribution of P is typically not uniform
across field plots. In addition, P deficiency often
occurs in conjunction with other stresses, such
as Fe or Al toxicity or drought, and, since these