1. Challenges for rice breeding Application of biotechnological tools
Dave Mackill
Plant Breeding, Genetics & Biochemistry Division
International Rice Research Institute
Los Baños, Philippines

2. Crop/soil/water management
IRRI MTP Programs
Program 1
Program 2
Program 3
Genetic Resources
and
Gene Discovery
Favorable
environments
Unfavorable
environments
Genetic improvement
Crop/soil/water management

3. Rice breeding activities
Irrigated breeding:
Indica varieties
New Plant Type
Hybrid rice
Temperate rice
Wide hybridization
Adverse soils
Molecular breeding
Transgenic breeding
Rainfed lowland
Upland
Deepwater/tidal
Aerobic rice
Favorable environments
Unfavorable environments

4. Important challenges for rice breeding
Water limitation
Micronutrient density (Fe/Zn, and Golden Rice)
Direct seeding (weed competition/anaerobic germination)
Abiotic stress (drought, submergence, salinity)
Increasing yield potential
Grain quality

5. Water scarcity

6. Aerobic rice varieties
Favorable upland varieties (Apo)
Hybrid rice varieties (Magat)
Irrigated rice varieties
Rainfed lowland varieties
Upland X Lowland hybrids

7. Aerobic rice yields, IRRI, 2001 ds
Cultivar
Yield DH
Magat
4.27 80
IR (Apo)
3.54
111
Maravilha
3.04
113
KMP 34
2.98 81
B6144
2.50
116
LSD
0.72 6

8. Some irrigated breeding lines have superior yields under aerobic conditions

9. Nutritious rice

10. Fe content in the hull, brown rice, hull and grain, and different plant parts.
(Fe mg/kg)
Brown rice =
Paddy =
Hull =

11. Effect of Soil Zn in the micronutrient loading in the grain

12. Direct seeding

13. Traits for direct seeding
Anaerobic germination tolerance
Good seedling vigor
Submergence tolerance
New Plant Type for higher yield

14. Anaerobic seeding

15. Abiotic stress tolerance

16. Abiotic stress breeding
Emphasis on drought, submergence, salinity (some soil difficiencies-P, Zn)
Conventional breeding, participatory varietal selection, QTL mapping
Functional genomics-identifying candidate genes and allele mining

17. Proteomics: salt tolerance
-2.5 -2
-1.5 -1
-0.5
0.5 1
1.5 2
2.5
CT9993
IR62266
IRL 20 17 28 37 3 14 15 26 40 22 23 4 11 31 36 42 13 6 9 21 24 30 32 34 35 38 39 41 12 25 5 7 10 8 16 18 19
Log2 ((abundance ratio)
Cyt TP
Rubisco activase
Ct FBP aldolase
Ct RNA binding protein
GSH- DHAR
S-like RNase
S-Like RNase
Cyt Cu-Zn SOD
EF-Tu
Rubisco Activase
NDK1
Ct Cu-Zn SOD
Ct Rieske FeS
Arabidopsis protein

18. Higher yield potential

19. Higher yield potential Original new plant type
Japonica type – high yield in temperate areas (China)
Susceptible to diseases/poor grain quality
Low biomass associated with low tillering

20. Two varieties released in China

21. Modified new plant type
Single cross with indica parents
Improved resistances
Long-grain, intermediate amylose
Higher yield in tropical environments
Retains larger panicle and strong stem

23. IR72
Improved NPT

24. Hybrid rice Still higher yield potential
Wider crosses show high potential (NPT)
Possibility in unfavorable environments (aerobic rice, salinity)

25. Wild species introgression

26. C4 rice?

27. Incorporating biotechnological tools
Transgenics
Introducing novel genes
Modifying rice genes
Combining multiple rice genes
Marker assisted selection
Conventional (linkage mapping)
Functional genomics

28. Major genes or QTLs Major gene traits QTLs
Backcrossing recessive genes
Pyramiding multiple genes
Difficult to measure traits
QTLs
Limited progress through conventional breeding

29. Why haven’t breeders taken advantage of QTLs identified in rice?
Poor resolution of agronomic QTLs
Small effects
Interaction with environment and genetic background
Expense of genotyping

30. In what situations would breeders be encouraged to select for QTLs?
QTL with relatively large effect
Traits difficult to measure
QTL effect independent of genetic background
QTL being transferred from an exotic source (ABQTL)

31. Current bottlenecks for rice breeding
Many rice varieties are released each year by national programs in Asia. Most of these varieties achieve limited success. A few become widely popular.

32. However, a relatively small number of cultivars have been adopted on large areas

33. It has become increasingly difficult to achieve further improvements
Widely grown varieties with favorable features are rare achievements
Most newly released varieties, while often showing superiority in breeders’ tests, do not replace the existing varieties

34. Making incremental improvements in these varieties is a viable breeding strategy
These varieties become increasingly prone to diseases and insect pests (maintenance breeding)
The varieties often lack tolerance to abiotic stresses, which limits their production to more favorable areas

35. Resistances to abiotic stresses
Highest level of tolerance often in exotic or and/or unproductive cultivars
Expensive and difficult to accurately evaluate
Improvements would have clear impacts on poorest farmers

36. Submergence tolerance as an example
ST was thought to be a quantitative trait of relatively high heritability based on at least 4 genetic studies up to 1995

37. Physical map of Sub1 SUB1 CEN NotI NotI NotI NotI NotI NotI 6 Recs
1 Rec? (42kb)
4 Recs (<110kb)
2 Recs
14A11-F15
14A11-481
14A11-L’’
14A11-270
20P2-F20
RZ698
13L11-L
14A11-L’
17P5-L
RAPD1
SSRA1
14A11-L
RAPD1’
RAPD1’’
A303
R71K
R50K
A209
R1164
NotI
NotI
NotI
NotI
NotI
NotI
20P2 (150kb)
TQR14A11 (99kb)
TQB7A1 (109kb)
TQR13L11 (75kb)
TQH17P54 (69kb)
TQH9D24 (69kb)
CEN
263 kb, completely sequenced

38. Traditional backcross
BC1
BC2
BC3
BC4
Traditional backcross
Percent recurrent parent genome
75.0
87.7
93.3
99.0
Percent recurrent parent genome
85.5
98.0
100
MAB
From Ribaut & Hoisington 1998 27

39. FL1 R
FL2
Number of individuals to obtain desired genotype in following BC generation d1 d2
d1 (cM)
d2 (cM)
From Frisch, Bohn & Melchinger 1999 29

40. FL1 R
FL2
Number of individuals to obtain desired genotype in following BC generation d1 d2
d1 (cM)
d2 (cM)
From Frisch, Bohn & Melchinger 1999 28

41. Target QTLs for Abiotic Stress Tolerance
Submergence tolerance (Xu and Mackill 1996)
Deepwater elongation (Sripongpangkul et al. 2002)
Drought (Babu et al. 2003)
Al toxicity (Nguyen et al. 2003; Wu et al. 2000)
P uptake (Wissuwa et al. 1998)
Salt tolerance (Bonilla et al. 2002)
Cold tolerance tolerance (Andaya and Mackill 2003)
Fe toxicity tolerance (Wan et al 2003)

42. P uptake 12 Pup1: LOD 16.5 R2 78.8 From Wissuwa & Ismail G124A (30.0)
C443 (50.5)
S10704 (49.3)
P96 (47.9)
C449 (72.5)
G2140 (63.7)
V124 (70.7)
S13126 (55.1)
S1436 (57.4)
S13752 (56.0)
C61722 (58.9)
C901
C449
W326
C2808
G2140
C443
S10520
G124A
S2572
C732
Pup1:
LOD 16.5
R2 78.8
From Wissuwa & Ismail

43. Fine mapping salinity tolerance gene
Chromosome 1
58.1
RM23
60.6 AP
62.5
AP ,RM3412
63.9 AP
Saltol
gene
64.9
RM140, S13927/AluI
65.4 AP
66.5
CP10135
67.6
AP ,
AP , RM8115
67.9
AP /DraI
73.7
RM113,RM24
LOD 6.7
R2 43.9
From G. Gregorio

44. Al toxicity
Nguyen, Brar

45. Cold tolerance 4 LOD 8.36, R2 20.8 12 LOD 20.34, R2 40.6
From Andaya & Mackill 2003

46. Maximizing the value of QTLs12 1
Allele mining