1. Developing climate change-ready and low-Input adapted rice
varieties for temperate regions
Increasing production cost relating to fertilization and irrigation are two of the main constraints in rice production. Moreover, the unpredictable weather
patterns and the increasing mean annual temperature due to climate change are limiting the yield potential in rice especially in temperate regions. It is
therefore essential to develop rice varieties which are climate-change ready and with high yield potential even under conditions of low input. Using molecular
breeding, we have been developing temperate rice varieties with introgressions of Pup1-OsPSTOL1 (Gamuyao et al. 2012, Nature) for enhanced early-root
vigor to enhance Phosphorus (P)-efficiency use under conditions of low P input and rainfed. Also, we have conducted QTL mapping for yield-elated traits
under low P and low water input during wet season of 2012 (WS) and dry season of 2013 (DS). Using 137 indica × japonica recombinant inbred lines (RILs),
we have identified 5 QTLs for panicle length on chromosomes 1 (QPL1.1 and QPL1.2), 2 (QPL2), 9 (QPL9), and 11 (QPL11), under rainfed conditions and low
phosphorus (P) input. These QTLs were not identified in temperate region (Korea) suggesting specificity to tropical conditions. Interestingly, QTLs for yield
components were collocated with these QTLs. We are now developing NILs with various combinations of these QTLs to confirm and fine-map the important
genomic regions. The yield advantage under low input of the developed lines versus lines without introgressions of QTL/gene is presented in this poster.
Ian Paul Navea1, Maria Stefanie Dwiyanti1, Reuben Jacob Labios1, Hee Jong Koh2, Woon-Chul Shin3, and
Joong Hyoun Chin2
1International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
2Division of Plant Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
3 Rural Development Administration, NICS, Sangju, South Korea
Email address: i.navea@irri.org
Materials and methods
Acknowledgments
This study was supported by a grant from the Next-Generation BioGreen 21 Program (Plant
Molecular Breeding Center, no. PJ009076), Rural Development Administration, Republic of Korea.
Special thanks to Brian Montes for the technical support.
Key results
P0046
Results and discussion
Plant Molecular
Breeding Center
Pup1 breeding
New low P and rainfed yield
QTL identification
Plant materials
Backcrossed populations (BC2F5):
 MS11
 Unkwangyeo
 Jinmibyeo
 Dasanbyeo
Pup1 donor:
 IR64-Pup1 F
137 F15:16 RILS derived
from a cross between
Dasanbyeo (tongil indica)
and TR22183 (temperate
japonica)
Phenotyping/
Screening
Data on yield-related traits were gathered from each line grown under Low P (No
P application for atleast 4 seasons) and rainfed rice fields in IRRI Philippines.
Molecular markers/
Foreground selection (Gel-based):
Background selection:
 Infinium™ 5K SNPs
 Agro-morphological resemblance to recipient
lines
384-plex indica-japonica
platform of BeadXpress™
Genotypic
analysis/QTL mapping
Foreground marker:
 Manual scoring was done for the gel pictures of
the samples using the foreground markers.
Background selection:
 GGT graphical software was utilized to asses
lines with the highest recovery of recurrent
parent genome.
Linkage mapping:
 Joinmap 2.0 using 234
SNP markers
polymorphic to
parents
QTL analysis:
 ICIM Mapping
(inclusive composite
interval mapping and
composite interval
mapping)
Pup1 breeding
New low P and rainfed QTL identification
Results and discussion
A
A. K20-2Bsp
B. K29-1
C. K46-1
B
C
Fig. 2. Panicles of
Dasanbyeo (left)
and TR22183
(right).
Fig. 3. Panicle length distribution of RILs.
0P60P
IR RF
DS
TR
WS
DS
Panicle length of TR22183 (TR) was consistently long in all treatments.
Dasanbyeo (DS) exhibited sensitivity to both P and water.
P and water effects among RIL
by ANOVA (data not shown)
 P effect was significant in the
vegetative and reproductive
stages except for days to
heading.
 Water effect was significant in
the late- and mid-vegetative
stage for WS and DS,
respectively.
 P × water interaction was
significant for panicle length
and grain yield.
Panicle length QTLs were identified in chromosomes 1,2,9, and 11 using 137 RILs.
 In the RILS, TR22183 allele increased panicle length and spikelet number in all QTLs
except QPL2.
 QPL1.1 and QPL11 were consistently identified in both WS and DS under low P input
and rainfed system.
 Yield component QTLs were collocated with the QPL regions.
 None of these QPL regions were identified in a parallel experiment in Korea (Data not
shown)
Abbreviations: rainfed (RF), irrigated (IR),panicle length
(pl), grain number (gn), spikelet number (sn), one-
hundred grain weight (hgw), grain yield from 5 bulked
plants (gy5), unfilled grains (ufg), tiller number at 40
days after transplanting (tn40)
Fig. 1. Mean yield of top 3 Pup1-introgression lines as
compared to the recurrent parent grown under low P
input and rainfed. Means with the same letter are not
significantly different within a population at α=95%, using
HSD.
Pup1 Program
Average yield (gm) gain
per plant
MS11 8.0
Jinmibyeo 7.0
Unwangbyeo 7.6
Dasanbyeo not significant
0
5
10
15
20
25
MS11
MS11-Pup1Line1
MS11-Pup1Line2
MS11-Pup1Line3
GrainyieldPlant-1(gm)
Line
0
5
10
15
20
25
Jinmibyeo
Jinmi-Pup1Line1
Jinmi-Pup1Line2
Jinmi-Pup1Line3
GrainyieldPlant-1(gm)
Line
c
a
ab
b
0
5
10
15
20
25
Unkwangbyeo
Unkwang-Pup1
Line1
Unkwang-Pup1
Line2
Unkwang-Pup1
Line3
GrainyieldPlant-1(gm)
Line
Background BC2F5 line DTH Plant height Fertility Panicle length
Panicle
number
Yield per
plant
MS11
MS11-Pup1 Line 1 ns ns ns ns ** (+) *** (+)
MS11-Pup1 Line 2 ns ns ns ns ** (+) ** (+)
MS11-Pup1 Line 3 ns ns ns ns * (+) ** (+)
Jinmibyeo
Jinmi-Pup1 Line 1 ns ns ns ns ** (+) ** (+)
Jinmi-Pup1 Line 2 ns ns ns ns ** (+) ** (+)
Jinmi-Pup1 Line 3 ns ns ns ns * (+) * (+)
Unkwangbyeo
Unkwang-Pup1 Line 1 ns ns ns ns ** (+) *** (+)
Unkwang-Pup1 Line 2 ns ns ns ns ** (+) ** (+)
Unkwang-Pup1 Line 3 ns ns ns ns ** (+) * (+)
Dasanbyeo ns ns ns ns ns ns
Pup1 introgression lines grown under low P input and rainfed had yield
advantage over the recurrent parent except for Dasanbyeo-Pup1 program
Table 1. Agronomic performance comparison of introgression lines vs recurrent parent under low P and rainfed
condition. *P<0.10 **P<0.05 ***P<0.001.
 Pup1 introgression in the temperate varieties had significant effect on yield
under low P and rainfed condition, except Dasanbyeo.
 We have identified 5 QTLs for panicle length under low P and rainfed
conditions using indica x japonica RILs. These QTLs were not identified in
temperate region suggesting specificity to tropical conditions.
 QPL1.1 and QPL11 were consistently identified across seasons. In both QTLs,
TR22183 increased the panicle length and spikelet number.
 Pyramiding of QTLs studied in the tropics could be essential in developing
rice varieties ready to climate change and low-input adapted.
QPL1.1
QPL1.2
QPL2
QPL11
QPL9