Drought is a major constraint affecting rice productivity in rainfed and upland ... Isaac Kofi Bimpong1, Evelyn M.T. Mendoza2, Rachid Serraj1, Merlyn S.
Identification of QTLs for agronomic traits under lowland drought stress in crosses of Oryza sativa x O. glaberrima Isaac Kofi Bimpong1, Evelyn M.T. Mendoza2, Rachid Serraj1, Merlyn S. Mendioro2, Joie Ramos1, Jose Hernandez2 and Darshan S Brar1 1 International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines 2 University of the Philippines Los Baños (UPLB), College, Laguna. Philippines
Drought is a major constraint affecting rice productivity in rainfed and upland ecosystems. It causes severe damage at different stages of rice growth, resulting in considerable yield loss. There is urgent need to develop rice varieties that use water efficiently and are tolerant to drought during different stages of crop growth. Only a limited genetic variability exists in indica rice for drought tolerance, however, O. glaberrima, the African indigenous rice species possesses resistance to stresses such as drought, blast, rice yellow mottle virus (RYMV), nematodes, and African gall midge (Jones et al 1997). In this study we explored O. glaberrima as a new donor for drought tolerance.
Objectives
•
To develop advanced backcross alien introgression lines (AILs) from crosses of O. sativa and O. glaberrima. To evaluate AILs for drought tolerance under field conditions. To identify QTLs for agronomic traits under drought stress.
• •
Materials and methods
• • •
45 QTLs for different agronomic traits of which 18 are new were identified. O. glaberrima contributed 67% alleles to the newly identified QTLs. One QTL at RM208 on chromosome 2 had positive effect on yield under stress accounting for 22% of the genetic variation.
x O. sativa
O. glaberrima
Mapping populations
513 AILs (BC2F3) Fig 3. New QTLs identified in IR64 x O. glaberrima BC2F3 Populations
•Among the high yielding group, strong LD between locus on
A subset of 200 AILs selected based on 10% extremes (best, poor & random AILs ) was used for genotyping
Field evaluation under drought stress
chromosome 4 and locus on chromosomes 3 and 7 were observed. Many loci on different chromosome exhibited low LD (Fig 4).
Two lowland nurseries Molecular analysis using 173 SSR and STS markers
•In the low yielding group, low LD between some loci on
Agronomic traits evaluated: Yield, harvest index, number of tillers, fertility , biomass, flowering and plant height
chromosome 4, lower arm of chromosomes 7, 10 and 11 were observed.
QTL analysis using QTLMapper 1.6 for single point and Mapmanager QTX 20 for interval mapping
1
1
2
Results and discussion
•
50 high yielding lines 50 High yielding lines selected from stress trial from stress trial
2
3
50 low yielding lines from stress trial 3
4
Thirty-three AILs showed higher yield per plant than the recurrent parent (Fig 1.).
4
5
5
6
6
7
7
8
8
9
9
Introgression Lines
10
10
11 12
25 20 15 10 5 0
11 12
Fig 4. Heatmap display of LD as R2 for all marker pair used in O. sativa x O. glaberrima AILs IR64
•Strong association of markers with traits was detected traits (harvest index, yield per plant, number of tillers, sterility) Table 1. 50-55
40-49
30-39
20-29
15-19
10-12,
Yield (gm/plant)
Fig 1. Frequency of 33 AILs with yield higher than IR64 (recurrent parent)
• O. glaberrima genome introgressed into O. sativa ranged from
•Markers S02085 and RM310 were strongly associated with yield. Table 2. 1. Marker-trait Marker traitassociation associations analysis for different drought traits AILs derived from x O. Table analysis for different drought relatedrelated traits in AILsin derived from IR64 x O.IR64 glaberrima glaberrima HI1
HI1
YPP1
YPP1
TN1
TN1
PS1
PS1
Chromosomes
Marker
-LOG(P)
r
-LOG(P)
r
-LOG(P)
r
-LOG(P)
r
1
RM562
2.8
0.26
1.9
0.2
1.3
0.16
2.2
-0.22
5.25% with a mean of 4.5% in all selected groups (Fig 2).
2
S02039
0.4
0.07
0.4
-0.07
0.2
-0.04
2
-0.21
2
S02085
1.8
0.19
9.1
0.48
4.2
0.32
1.8
-0.2
•No difference was observed in the extent of introgression among
3
S03010B
0.3
-0.06
0.2
0.04
0
0.01
2
0.21
4
S04077A
0.4
-0.07
0.3
0.06
0
-0.01
2
0.21
8
RM310
2.5
0.24
3.5
0.29
2.7
0.25
4.6
-0.34
AILs selected for yield
8
RM42
2.5
0.24
2.1
0.22
3.2
0.27
2
-0.21
11
RM202
0.4
-0.07
0.3
-0.05
0.4
-0.06
2.3
0.23
FDR thresh.
2.3
2.7
1.9
Displayed are the –10Log(P) values (–10Log transformations of the association probabilities) for markers on chromosome1,2,3,4,8 and 11. Markers are arranged (in map order) rows, traits are arranged in columns, Only markers with a significant marker-trait correlation for at least one of the traits are given.
30 Number of introgression lines
2
25
Conclusion
20
•33 AILs performed better under drought stress which need further
15 10 5 0 0~5%
5~10%
10~15%
15~20%
20~25%
Percent introgression of O. glaberrima segment Key: Black bar = HY lines from non stress, Blue bar = HY lines from stress & Red bar = LY lines from stress
Fig 2. Molecular analysis of selected AILs derived from O. sativa x O. glaberrima under drought stress from lowland trial
testing for use in breeding for drought tolerance. •QTLs identified under drought stress for yield particularly on chromosome 2 associated with RM208 would be useful for future research in marker – assisted selection
