Challenges for rice breeding Application of biotechnological tools Dave Mackill

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

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

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

4. 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 Important challenges for rice breeding

5. Water scarcity

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

7. Aerobic rice yields,IRRI, 2001 ds

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) 225 - 448 Brown rice = 10 -17 Paddy = 448 - 908 Hull = 1105 - 2010 247 - 520 174 - 310

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

12. Direct seeding

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

14. Anaerobic seeding

15. Abiotic stress tolerance

16. 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 Abiotic stress breeding

17. 2.5 CT9993 2 IR62266 1.5 1 0.5 Log2 ((abundance ratio) 0 -0.5 -1 -1.5 -2 -2.5 IRL GSH- DHAR Ct RNA binding protein S-like RNase S-Like RNase Cyt Cu-Zn SOD EF-Tu Cyt TP Rubisco activase Ct FBP aldolase Rubisco Activase Ct Rieske FeS Ct Rieske FeS Arabidopsis protein Ct Cu-Zn SOD NDK1 32 37 19 23 22 1 14 3 26 2 36 42 31 39 41 6 13 35 9 5 7 10 18 8 15 4 11 38 34 24 21 16 28 17 40 30 12 25 20 Proteomics: salt tolerance

18. Higher yield potential

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

20. Two varieties released in China

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

23. IR72 Improved NPT

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

25. Wild species introgression

26. C4 rice?

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

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

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

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

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

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

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

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

42. G124A (30.0) C732 S2572 S10520 (40.3) G124A S10520 P96 (47.9) C443 S10704 (49.3) C443 (50.5) S14025 (51.8) G2140 S13126 (55.1) S13752 (56.0) S1436 (57.4) C449 C61722 (58.9) G2140 (63.7) C2808 W326 V124 (70.7) C901 C449 (72.5) P uptake 12 Pup1: LOD 16.5 R2 78.8 From Wissuwa & Ismail

43. Fine mapping salinity tolerance gene Chromosome 1 58.1 RM23 60.6 AP3206-124201 62.5 AP4253-20757,RM3412 63.9 AP3722-9700 Saltol gene 64.9 RM140,S13927/AluI AP3211-28 65.4 66.5 CP10135 67.6 AP2869-104052, AP2869-17620, RM8115 67.9 AP3143-072/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 QTLs 12 1 Allele mining