GSR Breeding Strategy – Exploiting the  Hidden Reservoir of Diversity for  Improving Complex Traits in Rice          Zhi-K...
SubjectsIntroductionConcept of GSRGSR Breeding Strategy andTechnologyPerspectives
The impact of ‘Green Revolution’ in China        60000                 Impact of ‘Green Revolution’                       ...
Important problems in rice       production worldwide• Increasing problems in abiotic and biotic  stresses• Over-use of pe...
In ChinaCurrent agricultural practices: higher inputs-for high yields- polluted  environmentsChina consumes ~1/3 of the gl...
Trends of rice production and uses of pesticides                  and fertilizers in China in the last 30 years           ...
5              Grain yield(ton/hm2)                                                                      Grain yield per u...
Annual yield losses~20% from abiotic stress: drought,       problem soils, etc)~15% from biotic stress: diseasesand insect...
Water crisis and                                drought in ChinaFresh water resources per capita in China is less than aqu...
Which places have been left out by Green                         Revolution: Rice Yield Gaps in Irrigated and             ...
Consequences of the Green Revolution               Productivity                  Diversity
Chinese scientists are calling    “Second Green Revolution”   Less inputs, more production, and     environmental sustaina...
What are “GSR”?High yielding cultivars with multiple “Green”traits:Resistances/ tolerances to:Abiotic stresses: Drought, s...
To develop GSR rice varieties, breedersare facing the following challenges:    Many target traits:    Yield and its relate...
Where are the sources of genetic variation  for improving the    ‘green’ traits?
Rice Germplasm Collections in   Genebanks Worldwide: ~ 215,000 entries10% of 22 wild species                              ...
Status of the International Rice   Genebank Collection at IRRI                             Incoming                Accessi...
Characterization of O. sativa% accessions scored                        accessions (n=79,925)                100          ...
No. accessions                20,000                10,000                30,000                40,000        Blast   50,0...
Cold tolerance (1-3 = tolerant; 5 =    intermediate; 7-9 = susceptible)2,500            n=6,6252,0001,5001,000 500   0    ...
Yield responses of the 193 parental lines of IRMBN     to the terminal drought under the lowland condition25              ...
Establishment of the core collections for              major crops in the CAAS’s genebank      Core collections of rice, w...
Current Status of Characterization and Utilization of Germplasm Collections in Genebanks Worldwide  Collection and conserv...
Utilization – very poorly- Less than 5% of the collected germplasm in the Genebanks  have been utilized in the worldwide b...
The GSR Breeding Strategy: Exploiting the maximum genetic diversity in the      primary gene pool of riceObjectives To exa...
The Basic IdeaFull Exploitation of The Genetic Diversity in the          Primary Gene Pool of Rice
The GSR Breeding Strategy                          Recipients                            Donors                        (46...
The Chinese GSR research institutions - China National Rice Molecular Breeding Network
GoalThe goal of NCMBN was to developsuperior inbred and hybrid cropcultivars with significantly improvedyield stability, y...
Specific objectivesTo broaden the genetic base of crop cultivars in major cropgrowing areas of China by maximizing the gen...
Proof of the Concept
Two Fundamental Questions:• How much useful genetic diversity,  particular for the complex  phenotypes, within the primary...
Part I: Introgression breeding        and mass selectionRecurrent ParentsIR64 - Indica, high yield/widely adaptableNew Pla...
The “value” added and base broadening   approach – Introgression breeding    Widely         Add new genes/traits          ...
Procedure of the backcross breeding for development of ILs for               gene/QTL identification and cultivar developm...
Four Major Groups of Target Traits  Tolerances to abiotic stresses (drought,  salinity, low and high temperatures, N  and ...
Donor gene pool (203 accessions from34 countries)                  Sub-G1 (54)                   Sub-G2 (6)               ...
Gene diversity of the donor gene poolProportions of accessions Relative genetic diversity offrom different geographic   ac...
Target traits• Tolerances to drought, salinity, submergence,  zinc deficiency, phosphorus deficiency,  anaerobic germinati...
BC Breeding Procedure                     RP     X   Donors of diverse origins                           F1s X        RP  ...
Major differences of introgression breeding and             the conventional BC breeding                          BC breed...
Selection strategy for target    traits in random BC          progenies
Screening of BC2F2 populations for tolerance     to terminal drought at the reproductive stage             under the lowla...
Variation in BC2F2 populations for drought  tolerance under the lowland conditions
Summary of selected drought tolerant BC2F2 plants          under lowland stress conditions                         NPT    ...
The Screening of BC2F2 populations under upland drought conditions                          The RP, IR64
Summary of selected drought tolerant BC2F2 plants  under lowland stress conditions                           IR64         ...
Parental performances and 442 selected DT BC2F2plants for drought tolerance from 19 BC populationsVG Donors           Orig...
Screening of BC2F2 populations for salinity        tolerance at the seedling stageYoung seedlings were subjected to:      ...
Confirmation by progeny testingSeedling screening at EC 24 dSm-1 for 3 weeks
Table 1. Summary results of BC populations for screening salinity toleranceDetails                                   BC2F2...
Summary results of BC populations             for screening salinity tolerance                                    BC2F2 sc...
Screening of BC2F2 populations for  submergence tolerance in a deep-water pondThirty-five-day old seedlings were submerged...
Summary results of BC populations          for screening anaerobic germination               and submergence tolerance    ...
Screening of BC2F2 populations for           anaerobic germinationDirect seeding then submerged under 10 cm-deep water
Summary results of BC populations screened for anaerobicgermination and submergence tolerance Details                     ...
Screening for BPH Resistance       IR64
Summary results of BC populations screened for low temperaturegermination and brown planthopper resistanceDetails         ...
Summary results of BC populations for screening  low temperature germination and BPH resistance                           ...
Screening for tolerance to phosphorus                deficiencyTested in natural conditions in Pangil, Laguna.
Screening for tolerance to zinc deficiency
Summary results of BC populations screened for zinc deficiency tolerance                                                  ...
Selection for changed grain       type of Teqing
Selection for high       yield
High tiller number
Screening for blast resistance
Low N stressexperimentunder rain-offshelter
Improving japonica for coldtolerance at the reproductive stage
Screening results of 11 CY1 (recurrent parent) BC2F4 backcross populations for coldtolerance at the booting stage in 2008 ...
Screening of the BC2F4 bulk populations for cold tolerance                    (CT) at the booting stage:Seeds of the BC2F4...
Evaluation of 324 BC2F6 introgression lines and their recurrent parent, CY1 for cold tolerance of at the seedling and boot...
Comparison of selection efficiencies of 11 CY1 BC2F6 populations for cold                      tolerances at the seedling ...
Mean performances of 116 ILs of five populations for 11 traits evaluated under                normal and cold water stress...
The numbers of ILs from the 5 populations that deviated significantly CY1 for 11measured traits evaluated under cold water...
Mean performances of 19 promising ILs under cold water stress and                 normal conditions in 2009 and 2010 (Meng...
The hidden diversity for highlyheritable traits – BLB resistance
Reactions (lesion lengths) of HHZ and two donors to 14  tropical races of BLB caused by Xanthomonas oryzae pv oryzae      ...
8个黄华占群体对15个Xoo菌株产生反应类型                              (2012年8月,北京)F1-F5F1-     F6-        F6-F10   F11-                 F11-...
Blast evaluation of virulent strains   Evaluation of BB resistance of >500                                       lines (HH...
Ten HHZ ILs with broad spectrum resistance to all 14 races      of bacterial blight pathogen, Xanthomonas oryzae pv oryzae...
Reactions of 512 HHZ ILs to 14 tropical Xoo races            Race           R% (LL <3.0 cm)             P1                ...
Classification of 14 Xoo races into two major groups (virulent     and less virulent ones) based on the reactions of the 5...
Classification of the 512 ILs based on their resistances to the 14 Xoo Phillipines races                H9-39             ...
Are the parental performancescorrelated with the performances     of their BC progenies?
Genetic background effects in   introgression breeding
Submergence Tolerance    Number of submergence tolerant plants in 9 BC2F2    and 3 BC3F2 populations under the field condi...
Yield responses of the 193 parental lines of IRMBP     to the terminal drought under the lowland condition25              ...
Summary of selected drought tolerant BC2F2 plants         under lowland stress conditions                        NPT      ...
Parental performance and 442 selected DT BC2F2plants for drought tolerance from 19 BC populationsVG Donors           Origi...
Comparison of different IR64 and NPT BC generationsin screening for anaerobic germination (%)                             ...
Screening for seedling cold toleranceTwelve-day old seedlings were subjected to cold temperature for18 days at the mean da...
Seedling Cold Tolerance (from NARES)Selection of 861 C418 plants with seedling cold tolerance     from 28 C418 BC2F2 popul...
Genetic background effects on the   performance of BC progeniesTeqing / Chipda        NPT / Chipda
Donor and recipient effects on the number of BC2F2 plantsselected under lowland drought during the 2002 dry season Donor  ...
Genetic background effects on the number of survival plants under submergence      in 33 BC4F2 populations from crosses be...
Genetic background effects on the number of survival plants under submergence      in 33 BC4F2 populations from crosses be...
Can we develop ILs with extreme phenotypes for selected target            traits?
Screening results of 11 BC2F4 backcross populations derived from crosses between a     japonica variety, Chaoyou 1 (the re...
Table 6 Performances for AG of 11 promising BC4F3 lines and their donors    Recipient               Donor             Seed...
Trait specific introgression lines developed                        # of BC2F2      No. of selected   Target traits       ...
Summary of Selection Experiments• Most donors contributed performance enhancing  alleles to their BC progenies regardless ...
ConclusionsThere are tremendous amounts of hidden geneticdiversity in the current rice germplasmcollections for genetic im...
What are we going to do with   this large number of ILs?1. Direct development of new cultivars;2. As genetic stocks for di...
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
2012 GSR - breeding technology
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2012 GSR - breeding technology

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Lecture of Prof. Zhi Kang Li about rice breeding technology.

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2012 GSR - breeding technology

  1. 1. GSR Breeding Strategy – Exploiting the Hidden Reservoir of Diversity for Improving Complex Traits in Rice Zhi-Kang Li/CAAS GA biosynthetic pathway Geranylgeranyl diphospate AS CPS GA12 -aldehyde GA7ox ent - Copalyl diphosphate GA 12 KS KS GA13ox ent -Kaurene GA 53 ent -Kaurenol GA 15 GA 44 KO KO GA ent -Kaurenal C20ox GA 19 GA 24 sd-1 ent -Kaurenoic acid GA 9 GA 20 KAO KAO GA3ox ent -7a-hydroxy kaurenoic acid GA4 GA 1
  2. 2. SubjectsIntroductionConcept of GSRGSR Breeding Strategy andTechnologyPerspectives
  3. 3. The impact of ‘Green Revolution’ in China 60000 Impact of ‘Green Revolution’ Impact of hybrid rice 50000 40000 30000Yield 20000 10000 0 1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1988 1990 1992 1994 1996 1998 2000 2002 Year Yield/unit area Total production
  4. 4. Important problems in rice production worldwide• Increasing problems in abiotic and biotic stresses• Over-use of pesticides• Abuse of chemical fertilizers• Shortage of water• Ever increasing demands for yield increase• Urgent need for improved quality
  5. 5. In ChinaCurrent agricultural practices: higher inputs-for high yields- polluted environmentsChina consumes ~1/3 of the global production of chemical fertilizers and pesticides annually on only 7% of the world’s cultivated lands Fertilizer application and grain production in China Total grain production(in 10000 t)、unit area yield 4500 75000 production( 70000 4000 Fertilizer use 65000 Fertilizer use (in 10000t) 3500 Grain production Grain yield per unit area 60000 (kg/10ha) ) 3000 55000 )、unit 50000 2500 45000 )、 2000 40000 1500 35000 30000 1000 25000 500 20000 0 15000 1975 1978 1982 1985 1988 1991 1994 1997 2000
  6. 6. Trends of rice production and uses of pesticides and fertilizers in China in the last 30 years 40 150 50 Fertilizers (million ton) ) 7 35 单产 45 130 Pesticides(10000 ton) ) 农药 40Yield(ton/ha) (ton/ha) 30 化肥 110 6 35 25 90 30 20 ( 5 70 25 15 20 50 4 10 15 5 30 10 3 0 10 5 1978 1981 1984 1981 1984 1987 1990 1993 1996 1999 2002 2005 1975 1978 1987 1990 1993 1996 1999 2002 2005
  7. 7. 5 Grain yield(ton/hm2) Grain yield per unit area Grain yield/ha 4 / 3 2 1 1961 1966 1971 1976 1981 1986 1991 1996 2001 2006 350 350 350 350 Nitrogen use efficiency (kg/kg ) Nitrogen consumption(kg/hm2 ) 300 氮肥用量 300 300 300 )公顷) PFP 250 N consumption 250 kg/kg 250 250 / 200 NUE 200 200 200 氮肥生产效率(氮肥用量(公斤 150 150 150 150 100 100 100 100 50 50 50 50 0 0 0 0 1961 1966 1971 1976 1981 1986 1991 1996 2001 2006 1961 1966 1971 1976 1981 1986 1991 1996 2001 2006
  8. 8. Annual yield losses~20% from abiotic stress: drought, problem soils, etc)~15% from biotic stress: diseasesand insects, even with the heavy uses of pesticides.
  9. 9. Water crisis and drought in ChinaFresh water resources per capita in China is less than aquarter of the world average;Agriculture uses ~70% of the fresh water in China, andrice uses ~70% of the fresh water used in agriculture;Drought is occurring more frequently than ever before;Great yield loss of rice to drought in major rice areas.
  10. 10. Which places have been left out by Green Revolution: Rice Yield Gaps in Irrigated and Rainfed Ecosystems in Asia, 1967-97 6.0 Irrigated Rainfed 5.0 Irrigated 100 (40%) 4.0 80Y ie ld (t/h a ) Largely Irrigated (30%) 60 3.0 40 2.0 20 Rainfed 1.0 (30%) 0 MC TC 0.0 1967 1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 Adoption percentage Year of modern cultivars Source: M. Hossain, IRRI
  11. 11. Consequences of the Green Revolution Productivity Diversity
  12. 12. Chinese scientists are calling “Second Green Revolution” Less inputs, more production, and environmental sustainability 少投入、多产出、保护环境- to develop and widely adopted “Green Super Rice” that can produce high and stable yields under less inputs (chemical fertilizers, pesticides and water, and stress resilient).
  13. 13. What are “GSR”?High yielding cultivars with multiple “Green”traits:Resistances/ tolerances to:Abiotic stresses: Drought, salinity, alkalinity, etc.Diseases: Blast, bacterial blight, sheath blight, viruses, and false smut etcInsects: Brown plant hopper, stem borer, etcHigh resource-use efficiencies: Water andnutrients (N, P)
  14. 14. To develop GSR rice varieties, breedersare facing the following challenges: Many target traits: Yield and its related traits Stability - Resistances to biotic stresses - Tolerances to abiotic stresses Quality - Eating, cooking, and milling - Micronutrients
  15. 15. Where are the sources of genetic variation for improving the ‘green’ traits?
  16. 16. Rice Germplasm Collections in Genebanks Worldwide: ~ 215,000 entries10% of 22 wild species 27% of modern varieties 90% of the 73% of Cultivated rice landraces Everson et al. 1998
  17. 17. Status of the International Rice Genebank Collection at IRRI Incoming Accessions Total samplesO. sativa 85,999 15,784 101,783O. glaberrima 1,333 288 1,621Wild species 3,970 495 4,465Total 91,302 16,567 107,869
  18. 18. Characterization of O. sativa% accessions scored accessions (n=79,925) 100 90 80 70 60 50 40 30 20 10 0 44 morpho-agronomic traits
  19. 19. No. accessions 20,000 10,000 30,000 40,000 Blast 50,000 Bacterial blight Sheath blight Screened Rice tungro BPH 1 BPH 2 Resistant BPH 3 Green resistance/tolerances at IRRI leafhopperWhitebackedplanthopper Evaluation of rice germplasm for stress Cold tolerance
  20. 20. Cold tolerance (1-3 = tolerant; 5 = intermediate; 7-9 = susceptible)2,500 n=6,6252,0001,5001,000 500 0 1 3 5 7 9
  21. 21. Yield responses of the 193 parental lines of IRMBN to the terminal drought under the lowland condition25 ± -19.1±44.0%20151050 -100 -80 -60 -40 -20 0 20 40 60 80 100 120 140 160 Yield reduction (in %)
  22. 22. Establishment of the core collections for major crops in the CAAS’s genebank Core collections of rice, wheat, corn and Indica soybean were established with only 5% of the accessions representing over 90% Jap M. . Jap U. . Jap L. . genetic diversity of the whole collections. 0.1 0.1 Japonica Ind EM. . Ind M. . Ind M . L Basic Collections Core Collection Mini-core Accessions Entries sampling % Representation Entries sampling % Representation Rice 61479 3074 5% 89.9% 300 0.5% 66.6% Wheat 23135 1160 5% 90.1% 231 1.0% 69.1% Soybean 28809 1439 5% 91.0% 280 1.0% 71.0%Comparison of genetic diversity among core collectionswith different sampling ratio (Jia jizheng,2004)
  23. 23. Current Status of Characterization and Utilization of Germplasm Collections in Genebanks Worldwide Collection and conservation largely completed Characterization – very superficial - Phenotypic evaluation and description To identify accessions with desirable (often extreme) phenotypes to be used as parents in breeding programs - Few accessions with desirable phenotypes for most traits - No accessions with desirable phenotypes for certain traits How much valuable genetic variation for target traits in the primary gene pool for breeding remains unclear!
  24. 24. Utilization – very poorly- Less than 5% of the collected germplasm in the Genebanks have been utilized in the worldwide breeding programsReasons for Poor Utilization of Germplasm Outstanding commercial genotypes are commonly destroyed by crosses with unimproved exotic germplasm (Duvick 1984) Slow but consistent genetic improvement can still be achieved even within a narrow base in many breeding programs Selection of parental lines in breeding programs are largely based on phenotype and very few accessions appear to have “desirable” phenotype for complex traits
  25. 25. The GSR Breeding Strategy: Exploiting the maximum genetic diversity in the primary gene pool of riceObjectives To exam if there is sufficient (novel) genetic variation for target traits in the primary gene pool for most complex traits If yes, to develop an effective and efficient strategy to exploit the genetic diversity for complex traits - Integration with the molecular tools - Integration with gene discovery - Generation of information and training personnel
  26. 26. The Basic IdeaFull Exploitation of The Genetic Diversity in the Primary Gene Pool of Rice
  27. 27. The GSR Breeding Strategy Recipients Donors (46 best commercial X (203 WMCC, 300 CMC + Varieties and hybrid parents) 20 wild rice accessions) Genotyping by re- BC breeding to introgress sequencing of all superior alleles from MCC into parents elite genetic backgroundsParents for next Trait-specific Molecular database round of DQP IL sets in elite GBs of the parents Genotyping & phenotypingDevelopment of Genetic characterization new cultivars of ILs Breeding by MRS and PL sets or DQP -omics and bioiformatics Release to Theory and technology of farmers breeding by Gene networks and metabolic molecular design pathways of the target traits and functional diversity of alleles at the loci
  28. 28. The Chinese GSR research institutions - China National Rice Molecular Breeding Network
  29. 29. GoalThe goal of NCMBN was to developsuperior inbred and hybrid cropcultivars with significantly improvedyield stability, yield potential, andgrain quality for the major ricegrowing areas in China.
  30. 30. Specific objectivesTo broaden the genetic base of crop cultivars in major cropgrowing areas of China by maximizing the gene flow from theprimary rice gene pool into elite genetic backgrounds throughbackcross breeding;To exploit the hidden diversity of the primary rice gene poolfor improving complex target traits;To develop IL sets for important traits in elite rice geneticbackgrounds;To discover and characterize large numbers of QTLs andQTL networks underlying important traits, and to mineallelic diversity at important QTLs;To establish genetic/phenotypic database for the ILs;To train a new generation of molecular rice breeders in China.
  31. 31. Proof of the Concept
  32. 32. Two Fundamental Questions:• How much useful genetic diversity, particular for the complex phenotypes, within the primary gene pool of rice?• Can we combine the process of breeding with gene discovery (gene/QTL discovery and allelic mining)?
  33. 33. Part I: Introgression breeding and mass selectionRecurrent ParentsIR64 - Indica, high yield/widely adaptableNew Plant Type - Japonica, high yield potentialTeqing - Indica, high yield/widely adaptable
  34. 34. The “value” added and base broadening approach – Introgression breeding Widely Add new genes/traits IR64 introgression by backcross breeding adaptable lines with improved high yield target traitsvarieties (IR64) IR64 lines with improved Discovery of desirable QTLs usingtarget traits and the “same” DNA markers and MAS for pyramiding QTLs yield potential and quality
  35. 35. Procedure of the backcross breeding for development of ILs for gene/QTL identification and cultivar development RP x donors F1s x RP 25 BC1F1s x RP X Self and bulk harvest ~25 BC1F2s x RP ~25 BC2F1s x RP X Self and bulk harvest Bulk BC1F2 populations Bulk BC2F2 populations Screen fortarget traits: 1, 2, 3, 4, 5, n 1, 2, 3, 4, 5, n Replicated progeny testing for the introgression lines (ILs) for the selected target traits (tolerances to drought, salinity, submergence, BPH, etc), and for yield performances and other agronomic traits under non-stress conditions Large numbers of ILs with selected target traits in the elite RP genetic background Genotyped w/ DNA markers to track the gene flow and to identify genes/QTLs for the target traits Promising ILs with selected target Best ILs with selected target trait(s) trait(s) and good yield performances used as parental lines for nominated for NCTs pyramiding genes/QTLs from different donors Development and releases of green super rice cultivars for To rice farmers in the target specific target environments environments
  36. 36. Four Major Groups of Target Traits Tolerances to abiotic stresses (drought, salinity, low and high temperatures, N and P use efficiency, etc.) Resistances to biotic stresses (blast, sheath blight, false smut, BPH, stem borer, BB, etc.) Yield potential and heterosis Quality parameters
  37. 37. Donor gene pool (203 accessions from34 countries) Sub-G1 (54) Sub-G2 (6) I (indica) Sub-G3 (33) Sub-G4 (46) Ba-Bao-Mi (Yunnan) Sub-G5(15) II (japonica) Sub-G6 (12) Sub-G7 (28) Sub-G8 (9) III (New group) Jalmagna (India)
  38. 38. Gene diversity of the donor gene poolProportions of accessions Relative genetic diversity offrom different geographic accessions in different regions geographic regionsEurope America Others Europe America Others15% 10% NA NA SA SA China 33% China 40% 22% 26% SEA SEA 30% 24%
  39. 39. Target traits• Tolerances to drought, salinity, submergence, zinc deficiency, phosphorus deficiency, anaerobic germination, etc.• Resistances to BB, BPH, blast, tungro, sheath blight, etc.• Yield and related traits• Different maturities• Different types of grain quality parameters
  40. 40. BC Breeding Procedure RP X Donors of diverse origins F1s X RP BC1F1 X RP BC2F1 x BC2F2 bulk populations Selection for target traitsProgeny testing Survival plants Genotyping
  41. 41. Major differences of introgression breeding and the conventional BC breeding BC breeding Marker aided Introgression BC breeding breedingRP selection Elite Same SameDonor selection Yes Yes No/diverseTarget traits Single Single or few No limitation monogenic/dominantSelection Mass selection MAS Mass selectionProgeny testing yes yes yesPop. size Small Small RegularSelection efficiency High High DependsBreeding efficiency Low Low High
  42. 42. Selection strategy for target traits in random BC progenies
  43. 43. Screening of BC2F2 populations for tolerance to terminal drought at the reproductive stage under the lowland conditionsStress for 20 days (March 27,2001) Stress for 56 days (May 2, 2001)
  44. 44. Variation in BC2F2 populations for drought tolerance under the lowland conditions
  45. 45. Summary of selected drought tolerant BC2F2 plants under lowland stress conditions NPT IR64 Teqing Total Total plants selected 897 2775 489 4161 # of selected plants 8.5 22.4 6.3 13.2 per population (3.8%) (10.0%) (3.0%) (6.8%) Range 0 - 85 0 - 100 0 - 30 0 - 100 No. of populations 113 124 105 320 No. of I donors 59 67 59 185 No. of J donors 32 45 19 96Contributing donor (%) 80.5 90.3 74.3 87.8
  46. 46. The Screening of BC2F2 populations under upland drought conditions The RP, IR64
  47. 47. Summary of selected drought tolerant BC2F2 plants under lowland stress conditions IR64 Teqing TotalTotal plants selected 192 334 526 Ave. selected plants 9.6 (4.6%) 10.8 (5.2%) 10.3 (5.0%) Per population Range 4 - 20 3 - 15 4 - 30 No. of populations 20 31 51 No. of I donors 12 23 35 No. of J donors 8 8 16Contributing donor (%) 100 100 100
  48. 48. Parental performances and 442 selected DT BC2F2plants for drought tolerance from 19 BC populationsVG Donors Origin IR64 (S) Teqing (M) NPT(SS) Total LL (UL) LL (UL) LL I BR24 (S) Bangladesh 14 (27) 12 (7) 3 29 (34) I STYH (S) Myanmar 20 (26) - 4 24 (26) I OM1723 (S) Vietnam 7 (17) 7 (6) 0 14 (23) J FR13A (SS) India 15 (16) 17 (15) 0 32 (31) J Type3 (SS) India 23 (15) 10 (12) 0 33 (27) J Binam (M) Iran 20 (19) 14 (13) 1 35 (32) J HAN (M) China 11 (13) - 3 14 (13) I Zihui100 (S) China 8 - 9 17 J Khazar (S) Iran 58 - 58 Total 176 (133) 60 (53) 22 256 (186)
  49. 49. Screening of BC2F2 populations for salinity tolerance at the seedling stageYoung seedlings were subjected to: IR64 ST CK6 dSm-1 for 3 days, 12 dSm-1 for 2 weeks, 18 PokalidSm-1 for 1 week, and 24 dSm-1 for 1 week
  50. 50. Confirmation by progeny testingSeedling screening at EC 24 dSm-1 for 3 weeks
  51. 51. Table 1. Summary results of BC populations for screening salinity toleranceDetails BC2F2 screening BC2F3 reconfirmation IR64 Teqing NPT Total IR64 Teqing NPT TotalTotal BC2F2 populations 62 58 55 175 24 34 10 68Single plant selections per BCpopulation 4 - 12 4 - 13 1 - 14 0 - 43 0 - 49 0 - 11Total selected BC2F3 lines 490 428 374 1292 448 392 21 861Selection intensity (%) 3.95 3.69 3.40 3.69Number of indica donors 47 47 42 136 20 27 7 54Selected lines 369 345 289 1003 372 269 21 662Selection intensity (%) 4.39 3.67 3.44 3.69Number of japonica donors 9 9 7 25 3 6 1 10Selected lines 70 66 44 180 43 123 0 166Selection intensity (%) 3.89 3.67 3.14 3.60Number of intermediate donors 4 1 3 8 1 1 2 4Selected lines 35 5 19 59 33 0 0 33Selection intensity (%) 4.38 2.50 3.16 3.69
  52. 52. Summary results of BC populations for screening salinity tolerance BC2F2 screening BC2F3 reconfirmation IR64 Teqing NPT Total IR64 Teqing NPT Total# of BC2F2 pop. 62 58 55 175 24 34 10 68# of selections per pop. 4 - 12 4 - 13 1 - 14 1 - 14 0 - 43 0 - 49 0 - 11Total selected lines 490 428 374 1292 448 392 21 861# of contributingdonors 60 57 52 169SI (%) 3.95 3.69 3.40 3.69 For individual BC populations of 200 plants, a difference of 4% between two populations in selection intensity (survival rate) is statistically significant at P < 0.05 when the selection intensity is between 0.1 and 0.5.
  53. 53. Screening of BC2F2 populations for submergence tolerance in a deep-water pondThirty-five-day old seedlings were submerged under deep waterfor two weeks, then allowed to recover
  54. 54. Summary results of BC populations for screening anaerobic germination and submergence tolerance Anaerobic germination Submergence IR64 Teqing NPT Total IR64 Teqing NPT Total# of BC pop. 47 47 36 130 60 57 62 179# of selections per pop. 0-5 0-6 0 - 14 0 - 15 3 - 13 0 - 12Total selected lines 47 81 215 343 652 483 530 1665# of contributingdonors 46 46 35 127 59 57 60 176SI (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93
  55. 55. Screening of BC2F2 populations for anaerobic germinationDirect seeding then submerged under 10 cm-deep water
  56. 56. Summary results of BC populations screened for anaerobicgermination and submergence tolerance Details Anaerobic germination Submergence IR64 Teqing NPT Total IR64 Teqing NPT Total Total BC2F2 populations 47 47 36 130 60 57 62 179 Single plant selections per BC population 0-5 0-6 0 - 14 0 - 15 3 - 13 0 - 12 Total selected BC2F3 lines 47 81 215 343 652 483 530 1665 Selection intensity (%) 0.52 0.93 3.11 1.32 1.08 0.85 0.85 0.93 Number of indica donors 37 38 29 104 47 50 50 147 Selected lines 31 67 77 175 538 431 451 1411 Selection intensity (%) 0.43 0.90 3.10 0.84 1.15 0.86 0.90 0.96 Number of japonica donors 6 8 5 19 8 7 7 22 Selected lines 11 14 31 56 83 52 63 198 Selection intensity (%) 0.91 1.03 3.10 1.47 1.00 0.74 0.90 0.90 Number of intermediate donors 3 0 1 4 4 0 3 7 Selected lines 5 0 7 12 40 0 16 56 Selection intensity (%) 0.83 0.00 3.50 1.50 1.04 0.00 0.53 0.80
  57. 57. Screening for BPH Resistance IR64
  58. 58. Summary results of BC populations screened for low temperaturegermination and brown planthopper resistanceDetails Low temperature germination Brown planthopper resistance IR64 TQ NPT Total IR64 TQ NPT TotalTotal BC2F2 populations 14 15 10 39 64 67 62 193Single plant selections per BCpopulation 0 - 21 0 - 18 0 - 31 0 - 22 0 - 22 0-2Total selected BC2F3 lines 79 77 51 207 652 255 2 909Selection intensity (%) 5.64 5.13 5.10 5.31 10.19 3.81 0.03 4.71Number of indica donors 1 1 0 2 49 60 49 158Selected lines 0 3 0 3 565 221 2 788Selection intensity (%) 0.00 3.0 0.00 1.5 11.53 3.68 0.04 4.99Number of japonica donors 9 11 7 27 9 11 7 27Selected lines 55 52 39 146 54 21 0 75Selection intensity (%) 6.11 4.73 5.57 5.41 6.00 1.91 0.00 2.78Number of intermediate donors 4 3 3 10 4 3 3 10Selected lines 24 22 12 58 33 2 0 35Selection intensity (%) 6.00 7.33 4.00 5.80 8.25 0.67 0.00 3.50 For individual BC populations of 100 plants, a difference of 2.5% between two populations in selection intensity (survival rate) is statistically significant at P < 0.05 when the selection intensity is < 0.1.
  59. 59. Summary results of BC populations for screening low temperature germination and BPH resistance Low temperature germination BHP resistance IR64 Teqing NPT Total IR64 Teqing NPT Total# of BC2F2 pop. 14 15 10 39 64 74 62 200# of selections per pop. 0 - 21 0 - 18 0 - 31 0 - 22 0 - 22 0-2Total selected lines 79 77 51 207 652 255 2 909# of contributingdonors 14 14 10 38 62 67 59 189SI (%) 5.64 5.13 5.10 5.31 10.19 3.81 0.03 4.71 For individual BC populations of 200 plants, a difference of 4% between two populations in selection intensity (survival rate) is statistically significant at P < 0.05 when the selection intensity is between 0.1 and 0.5.
  60. 60. Screening for tolerance to phosphorus deficiencyTested in natural conditions in Pangil, Laguna.
  61. 61. Screening for tolerance to zinc deficiency
  62. 62. Summary results of BC populations screened for zinc deficiency tolerance BC2F4 progeny testing under very severeDetails BC2F2 screening under moderate field stress field stress IR64 Teqing NPT Total IR64 Teqing NPT TotalTotal number of BC populations 51 42 36 129 11 21 10 42Single plant selections per BCpopulation 4 - 12 2 - 12 0 - 12 0 - 12 0 - 10 0 - 15 0Total selected BC2F3 lines 454 383 324 1161 72 255 0 327Selection intensity (%) 7.42 7.60 7.50 7.50 2.14 2.41 0.00 2.01Number of indica donors 40 33 25 98 9 17 9 35Selected lines 370 320 237 927 63 200 0 263Selection intensity (%) 7.77 8.08 7.90 7.88 2.07 2.31 0.00 1.91Number of japonica donors 7 6 7 20 1 4 1 6Selected lines 63 63 84 210 0 55 0 55Selection intensity (%) 7.50 8.75 7.86 8.75 0.00 2.86 0.00 2.29Number of intermediate donors 3 - 1 4 1 0 0 1Selected lines 21 - 9 30 9 0 0 9Selection intensity (%) 5.83 - 7.50 6.25 5.63 0.00 0.00 5.63
  63. 63. Selection for changed grain type of Teqing
  64. 64. Selection for high yield
  65. 65. High tiller number
  66. 66. Screening for blast resistance
  67. 67. Low N stressexperimentunder rain-offshelter
  68. 68. Improving japonica for coldtolerance at the reproductive stage
  69. 69. Screening results of 11 CY1 (recurrent parent) BC2F4 backcross populations for coldtolerance at the booting stage in 2008 (1 SI = selection intensity, SF = spikeletfertility; 2 Different letters indicate statistical significance at P < 0.05, based on theDuncan testing) No. of SF (%) Population SI 1 Donor parent Subspecies Code selected size plants (%) Mean ± SD2 Range Bg90-2 Indica A 450 41 9.1 63.3±8.4D 50.3-86.5 X21 Indica B 450 29 6.4 64.3±9.9CD 50.6-87.1 X22 Indica C 450 28 6.2 65.6±10.1BCD 50.7-87.3 Q5 Indica D 450 31 6.9 71.1±11.1ABC 50.9-91.4 Chhomrong Japonica E 450 24 5.3 75.6± 51.4-87.8 Doddi Indica F 450 25 5.6 71.0±10.0ABC 50.2-90.0 Fengaizhan Indica G 450 44 9.8 74.1± 52.2-98.5 Shennong265 Japonica H 450 21 4.7 69.2±11.4ABCD 50.7-93.8 Yuanjing7 Japonica I 450 41 9.1 71.1±9.8ABC 50.0-90.1 OM997 Indica J 450 21 4.7 72.1±9.1AB 54.9-89.6 Cs94 Indica K 450 19 4.2 64.2±8.6CD 51.4-86.0 Mean 450 29.5 6.5 69.2±4.2 CY1 Japonica 324 24.8±4.3E 19.0-30.0
  70. 70. Screening of the BC2F4 bulk populations for cold tolerance (CT) at the booting stage:Seeds of the BC2F4 bulk populations were sown in the seedling nursery on April15, 2008, and 450 40-day old seedlings of each BC2F4 bulk population weretransplanted into a 45-row plot with 10 plants in each row and a spacing was25×15cm in the sheltered water pond of JAAS on May 25. Two rows of CY1were also transplanted on both sides of each plot as the checks. The water-pondwere irrigated with water of normal temperature (25~28℃). When CY1 enteredthe stage of panicle initiation, the LT treatment was initiated by irrigation offlowing cold water (19±0.5℃), which was adjusted in a nearby water pool by ℃mixing cold underground water (9℃) with the river water. The depth of the ℃cold water in the pond was 20cm and the treatment was maintained for ~30days until panicles of almost all plants exerted completely. Then, irrigationwith normal temperature water was resumed until the maturity. At thematurity, all plants except those with >3 days earlier heading or those with>3 days delayed heading than CY1 were harvested for measuring thespikelet fertility. Under this LT treatment, CY1 had a spikelet fertility of ±24.8±4.3%, then, any plant with spikelet fertility >50% were selected.
  71. 71. Evaluation of 324 BC2F6 introgression lines and their recurrent parent, CY1 for cold tolerance of at the seedling and booting stages in 2009 (SNP = spikelet number per panicle, FGN = filled grain number per panicle, SF = spikelet fertility) Cold stress at the seedling No. of stage Cold stress at the reproductive stageDonor parent selected Survival rate of seedlings lines (%) SNP FGN SF (%) Mean Range Mean Range Mean Range Mean Range BG90-2 41 19.5 10.0~62.5 114.5 76.3~164.2 55.0 22.1~95.7 48.0 18.5~71.3 X21 29 19.4 11.1~40.3 99.7 73.3~125.0 50.5 29.5~90.3 50.3 30.9~74.9 X22 28 19.6 12.5~40.7 113.2 70.3~139.0 58.5 4.5~94.9 51.4 5.6~79.4 Q5 31 18.3 15.0~33.8 114.6 68.3~185.4 56.5 15.3~113.6 49.2 14.6~83.6Chhomromg 24 17.0 15.0~32.5 109.8 77.6~175.2 74.0 47.0~104.8 66.9 45.6~83.4 Doddi 25 17.3 12.5~25.0 112.9 89.4~182.6 73.9 51.5~108.5 65.4 48.7~80.6 Fengaizhan 44 16.7 12.5~25.0 96.5 70.2~115.1 67.1 14.3~96.0 70.1 12.7~86.1Shennong265 21 15.6 0.0~23.3 96.9 65.0~144.8 62.0 36.9~99.2 63.0 40.0~79.9 Yuanjing7 41 18.5 15.0~45.0 116.0 93.5~151.0 80.6 30.4~106.4 69.2 25.5~84.2 OM997 21 37.1 15.0~82.4 81.6 56.2~108.1 42.0 14.9~64.0 51.1 23.3~72.0 Cs94 19 22.3 15.0~42.5 113.3 82.0~137.9 69.5 31.8~99.4 60.0 34.2~75.5 CY1 14.8 10.8~20.0 106.6 98.6~114.6 36.7 32.7~40.8 35.1 33.7~36.5 LSD0.05 4.5 8.3 8.2 6.2
  72. 72. Comparison of selection efficiencies of 11 CY1 BC2F6 populations for cold tolerances at the seedling and reproductive stages The reproductive stage The seedling stage Population N1 FGN SNP SF (%) SR (%) Code Donor N1 N2 N1 N2 N1 N2 N1 N2 A BG90-2 41 18 0 13 6 17 1 5 0 B X21 29 7 0 0 3 15 0 4 0 C X22 28 17 2 8 1 17 3 5 0 D Q5 31 15 2 10 4 20 3 1 0 E Chhomromg 24 17 0 7 3 22 0 2 0 F Doddi 25 23 0 1 0 24 0 0 0 G Fengaizhan 44 35 1 0 7 42 1 0 0 H Shennong265 21 12 0 2 9 18 0 0 1 I Yuanjing7 41 40 0 9 0 40 0 3 0 J OM997 21 2 1 0 13 13 0 14 0 K Cs94 19 14 0 5 1 14 0 6 0 Total 324 200 6 55 47 242 8 40 11N is the total number of selections based on single plant spikelet fertility (SF) in BC2F4 populations from Table 1, N1 and N2 are the numbers of the BC2F6 linesshowing significantly higher or significantly lower than CY1 for the measured traits. FGN, SNP, SF and SR are filled grain number per panicle, spikelet numberper panicle, spikelet fertility and survival rate of seedlings.
  73. 73. Mean performances of 116 ILs of five populations for 11 traits evaluated under normal and cold water stress conditions in 2010 Trait 1 Chhomrong Doddi Fengaizhan Shennong265 Yuanjing7 Mean CK N 24 24 24 20 24 116Under the normal conditions PH (cm) ± 135.2±4.4 ± 130.6±5.8 ± 125.7±5.4 ± 127.2±3.7 ± 132.3±4.5 130.3 117.1 BM (g/plant) 37.1±3.3 36.5±3.4 38.1±3.5 33.5±3.3 35.1±2.4 36.2 34.7 FGN 143.4±15.0 143.7±17.2 148.1±12.3 135.1±15.6 ± 156.3±19.4 145.7 138.9 SNP 176.6±20.8 179.4±20.9 171.2±17.4 172.9±17.7 ± 197.2±21.8 179.7 168.6 SF (%) 81.6±6.6 80.4±8.1 ± 86.9±5.8 78.4±7.2 79.2±5.3 81.4 82.4 GY (g/plant) ± 19.4±2.94 20.5-3.0 ± 20.9±2.5 ± 18.7±2.5 ± 18.7±2.7 19.6 19.7 HI (%) 55.0±5.2 59.1±4.9 57.9±3.7 59.1±4.4 56.0±4.8 57.3 60.3 PN 5.4±0.6 5.7±0.4 5.7±0.6 5.6±0.7 ± 4.8±0.5 5.5 5.7 GW (g) 24.3±1.5 ± 26.3±1.6 ± 22.0±2.1 24.5±1.1 ± 26.3±1.4 24.7 24.9 HD (d) 113.9±3.3 113.0±4.1 116.3±6.0 112.5±4.7 113.6±3.9 113.9 111.1Under the cold water stress PH (cm) ± 118.1±7.9 ± 119.9±7.7 ± 119.8±7.7 ± 122.4±6.6 ± 125.2±5.7 121.0 107.8 BM (g/plant) 16.2±3.2 16.1±2.7 16.8±2.5 15.3±3.6 17.5±3.6 16.4 12.0 FGN 46.8±28.4 39.1±20.2 ± 63.8±14.3 ± 22.9±14.1 46.4±19.8 44.5 12.8 SNP 118.9±23.9 121.7±13.8 110.4±12.9 117.7±24.1 139.6±19.6 121.8 121.5 SF (%) 38.8±18.3 32.3±14.5 ± 57.3±10.3 ± 19.7±12.1 33.3±14.6 36.9 10.5 GY (g/plant) ± 3.5±2.2 ± 3.0±1.7 ± 5.0±1.3 ± 1.9±1.2 ± 3.6±1.9 3.5 1.0 HI (%) 33.3±7.6 30.7±6.7 ± 40.9±4.4 ± 25.8±7.2 30.8±5.1 32.5 25.1 PN 3.3±0.5 3.4±0.6 3.3±0.5 3.7±0.9 3.2±0.5 3.4 3.5 GW (g) 17.9±1.5 18.0±1.6 17.5±2.7 17.1±0.9 17.9±1.3 17.7 16.4 HD (d) 131.3±2.2 128.2±3.3 132.0±4.1 126.9±4.1 128.6±3.0 129.5 125.2
  74. 74. The numbers of ILs from the 5 populations that deviated significantly CY1 for 11measured traits evaluated under cold water stress (S) and normal (N) conditions in 2010 GY GW HD HI PH SF BM (g/plant) FGN PN SNP Donor N1 Treat (g/plant) (g) (d) (%) (cm) (%) N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2Chhomrong 24 18 0 18 0 14 0 15 0 24 0 14 0 19 2 3 8 21 0 6 12 Doddi 24 18 0 19 0 15 0 16 1 16 2 14 2 21 0 5 7 19 0 4 4Fengaizhan 24 S 22 0 24 0 23 0 6 3 22 1 24 0 20 0 2 6 24 0 0 12Shennong26 5 20 12 1 7 0 6 0 5 2 10 8 7 6 18 0 9 5 10 0 6 8 Yuanjing7 24 21 0 21 0 19 0 17 0 16 0 15 1 24 0 3 8 20 0 12 1 Total 116 91 1 89 0 77 0 59 6 88 11 74 9 102 2 22 34 94 0 28 38Chhomrong 24 15 2 11 5 9 8 4 13 13 2 1 16 24 0 3 9 7 9 11 4 Doddi 24 11 4 10 5 9 5 17 4 11 3 6 7 24 0 4 4 8 12 13 5Fengaizhan 24 16 0 14 2 9 1 2 20 19 3 3 15 21 0 5 7 15 4 8 8 NShennong26 5 20 3 8 5 7 2 9 5 10 8 7 5 7 20 0 8 10 5 13 9 7 Yuanjing7 24 5 3 17 2 5 14 18 2 11 3 3 18 24 0 0 21 4 12 20 1 Total 116 50 17 57 21 34 37 46 49 62 18 18 63 113 0 20 51 39 50 61 251N is the total number of ILs with CT selected from each population; N1 and N2 are the numbers of the ILs showing significantly higher and lower traitvalues than CY1.GY = grain yield, BM = biomass, PH = plant height, PL = panicle length, PN = panicle number per plant, FGN = filled grain number per panicle, SNP =spikelet number per panicle, SF = spikelet fertility, HD = heading date, GW = 1000-grain weight, HI = harvest index.
  75. 75. Mean performances of 19 promising ILs under cold water stress and normal conditions in 2009 and 2010 (Meng et al. 2012) Line# Pop.1 2010 under the normal condition 2010 under cold water stress 2009 under stress PH BM SNP SF GY HI PN GW HD PH BM SNP SF GY HI PN GW HD SNP SF SRCK(CY1) 117.1 34.7 168.6 82.4 19.7 60.3 5.7 24.9 111.1 107.8 12.0 121.5 10.5 1.0 25.1 3.5 16.4 125.2 106.6 35.1 14.8LW213 G 134.2 48.5 192.3 91.1 28.1 60.1 6.4 22.8 103.0 129.2 19.5 131.2 69.1 7.2 46.8 3.5 15.7 128.0 101.7 81.2 12.5LW164 F 126.5 45.7 204.5 87.8 28.5 65.2 6.4 23.5 117.0 118.8 17.2 120.0 27.3 2.5 26.0 3.3 16.1 129.0 113.2 56.9 15.0LW180 F 131.7 38.8 182.0 89.8 23.4 63.1 5.7 25.6 101.0 131.7 18.0 138.0 39.6 4.9 36.3 3.3 19.1 123.0 107.3 68.0 17.5LW157 F 133.4 41.0 218.7 71.9 23.4 59.9 6.0 25.2 116.0 114.8 20.9 132.8 40.1 5.0 33.8 4.3 17.1 131.0 110.6 60.3 17.5LW170 F 129.3 40.0 183.3 83.7 22.8 59.7 5.9 24.0 117.0 117.8 19.6 119.5 45.5 5.3 38.4 4.8 16.7 131.0 118.4 71.9 17.5LW214 G 122.0 38.0 159.8 85.6 22.9 63.5 6.7 17.9 120.0 108.5 14.3 103.7 54.9 4.5 44.4 3.3 16.3 137.0 86.7 84.5 15.0LW188 G 121.0 40.1 164.3 84.2 23.1 60.6 6.7 21.0 121.0 130.0 16.6 119.7 66.9 5.8 46.2 3.2 17.0 138.0 90.9 82.5 15.0LW142 E 136.7 39.3 162.7 79.2 21.5 57.7 6.7 23.9 112.0 121.5 16.7 119.8 61.6 5.2 43.1 3.2 18.1 134.0 91.2 60.0 15.0LW154 E 137.8 39.9 198.3 82.9 21.9 58.0 5.4 23.4 112.0 128.5 19.7 160.7 67.4 7.4 47.7 3.0 17.4 130.0 121.6 71.3 15.0LW174 F 129.5 37.6 151.3 86.6 21.7 61.0 6.7 25.9 115.0 120.3 17.7 122.0 48.2 5.3 41.4 4.2 17.8 128.0 126.2 80.3 25.0LW207 G 132.6 40.0 192.8 79.9 22.1 58.0 5.8 21.2 121.0 127.0 20.1 118.3 66.6 6.7 43.1 3.8 17.5 132.0 115.1 83.7 20.0LW264 I 138.8 40.7 221.5 77.7 22.6 58.0 5.3 24.9 107.0 130.0 17.2 169.2 26.3 3.1 29.1 2.8 17.9 125.0 120.3 79.1 42.5LW250 I 130.7 39.2 226.8 79.9 23.3 62.6 5.2 26.0 110.0 136.8 20.1 136.8 65.1 5.8 38.4 2.7 18.0 132.0 108.4 76.1 20.0LW156 E 138.9 40.3 187.8 78.9 21.0 55.0 5.7 23.0 114.0 127.0 20.2 129.7 57.9 6.8 43.0 4.0 16.3 129.0 131.8 74.0 15.0LW151 E 131.9 37.7 168.3 82.9 19.2 53.9 5.6 24.2 114.0 122.3 19.3 123.5 67.2 6.6 43.3 3.3 16.6 130.0 122.4 82.9 16.3LW189 G 132.4 37.9 198.3 84.4 20.1 55.9 4.8 21.7 120.0 133.2 19.0 114.7 59.5 6.2 41.1 3.5 17.0 137.0 103.4 75.7 20.0LW216 G 129.1 37.3 170.8 87.1 20.1 56.9 5.4 20.7 123.0 111.8 17.1 99.8 51.7 4.3 34.4 2.8 15.9 139.0 99.9 86.1 16.9LW200 G 127.7 38.6 167.8 88.8 20.5 56.1 5.6 20.3 115.0 122.0 16.4 100.2 66.2 4.9 41.9 3.3 16.5 130.0 93.7 84.2 17.5LW291 I 121.1 33.1 181.5 84.8 17.5 56.5 4.7 25.1 120.0 126.3 24.9 156.3 39.1 6.6 32.2 4.2 17.7 131.0 143.6 74.5 45.0LSD0.05 1.9 2.1 8.2 2.6 1.6 1.8 0.3 0.5 1.9 3.7 1.8 11.1 8.1 1.2 4.3 0.4 1.1 1.6 8.2 6.2 4.5
  76. 76. The hidden diversity for highlyheritable traits – BLB resistance
  77. 77. Reactions (lesion lengths) of HHZ and two donors to 14 tropical races of BLB caused by Xanthomonas oryzae pv oryzae P1 P2 P3b P3c P4 P5 P6 P7 P8 P9a P10 P9c P9b P9d PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO PXO aver 61 86 79 340 71 112 99 145 280 339 341 347 349 363 ageHHZ 9.8 21.2 13.1 25.7 10.4 2.4 29.6 5.0 8.6 28.8 8.4 26.6 15.2 24.6 16.4PSBRC66 6.4 18.5 16.4 21.4 11.6 0.7 13.0 2.6 8.8 4.1 7.0 12.0 3.4 17.3 10.2PSBRC28 2.8 20.3 21.6 24.0 11.2 3.9 22.4 4.7 9.2 26.0 8.5 23.7 22.9 21.9 15.9
  78. 78. 8个黄华占群体对15个Xoo菌株产生反应类型 (2012年8月,北京)F1-F5F1- F6- F6-F10 F11- F11-F15 F1- F1-F5 F6- F6-F10 F11- F11-F15 F1-F5 F1- F6- F6-F10 F11-F15 F11-对部分小种抗病的株系 对全部15个小种高抗的株系 对全部15个小种感病的株系
  79. 79. Blast evaluation of virulent strains Evaluation of BB resistance of >500 lines (HHZ background) against 14 strains of 10 Xoo races, 2010 WS HHZ is susceptible to most tropic BLB races Vera Cruz et al
  80. 80. Ten HHZ ILs with broad spectrum resistance to all 14 races of bacterial blight pathogen, Xanthomonas oryzae pv oryzae PX PX PX PX PX PX PX PX PX PX PX PX O34 PX O11 PX O14 O28 O33 O34 O34 O34 O36 aver O61 O86 O79 0 O71 2 O99 5 0 9 1 7 9 3 ageHHZ 9.8 21.2 13.1 25.7 10.4 2.4 29.6 5.0 8.6 28.8 8.4 26.6 15.2 24.6 16.4PSBRC66 6.4 18.5 16.4 21.4 11.6 0.7 13.0 2.6 8.8 4.1 7.0 12.0 3.4 17.3 10.2HHZ15-SAL13-Y2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ15-SAL-13-Y3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ15-DT7-SAL1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ15-DT7-SAL3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ15-DT7-SAL6 0.2 0.2 0.2 0.2 9.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.9PSBRC28 2.8 20.3 21.6 24.0 11.2 3.9 22.4 4.7 9.2 26.0 8.5 23.7 22.9 21.9 15.9HHZ19-SAL-14-Y3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ19-DT8-SAL2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2HHZ19-SAL12-SAL4 0.2 0.7 0.9 0.5 0.2 0.2 0.2 0.2 0.4 0.2 0.3 0.9 0.2 0.2 0.4HHZ19-SAL14-SAL4 0.2 1.0 0.6 0.3 0.2 0.2 0.2 0.2 0.3 0.2 0.7 0.2 0.2 0.2 0.3HHZ19-SAL15-SAL2 0.2 3.8 2.2 0.6 0.4 0.4 0.8 0.5 0.3 0.3 0.3 0.6 0.4 0.4 0.8
  81. 81. Reactions of 512 HHZ ILs to 14 tropical Xoo races Race R% (LL <3.0 cm) P1 76.4 P2 4.7 P3b 4.9 P3c 4.9 P4 22.4 P5 78.4 P6 5.1 P7 46.6 P8 31.0 P9a 12.3 P10 12.1 P9c 4.7 P9b 5.1 P9d 50.8
  82. 82. Classification of 14 Xoo races into two major groups (virulent and less virulent ones) based on the reactions of the 512 HHZ ILs P1 P5 Weak virulence group P4 P7Name Xoo races P8 P10 P2 P9c P6 P3c High virulence group P3b P9a P9b 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 Average Distance Between Clusters
  83. 83. Classification of the 512 ILs based on their resistances to the 14 Xoo Phillipines races H9-39 H5-1 H8-27 H9-20 H17-65 H9-3 H9-13 H5-32 H8-44 H15-12 H17-29 H5-49 H15-1 H8-8 H8-23 H9-7 H8-13 H8-51 H9-16 H9-26 H5-12 H5-13 H8-3 H19-48 H17-11 H12-27 H8-33 H5-5 H15-26 H9-24 H5-51 H8-21 H8-31 H5-59 H8-47 H9-14 H9-25 H5-6 H8-41 H9-18 H8-40 H8-26 H12-17 H19-18 H9-56 H19-22 H19-23 H5-26 H17-32 H11-10 H12-26 H9-40 H8-55 H12-16 H11-32 H11-30 H11-36 H11-34 H11-45 H11-49 H12-39 H19-45 H12-2 H11-28 H9-70 H15-43 H17-35 H19-55 H19-13 H11-31 H19-15 H12-24 H9-41 H12-20 H19-46 H12-18 H19-29 H9-51 H11-16 H19-14 H17-34 H9-9 H8-38 H11-50 H12-40 H12-61 H12-55 H17-5 H15-19 H12-64 H15-21 H19-57 H19-50 H9-66 H19-59 H19-36 H15-8 H15-25 H12-54 H15-24 H19-56 H17-53 H9-4 H15-30 H5-55 H8-18 H15-11 H12-31 H5-60Name of lines H8-54 H11-54 H12-36 H19-35 H11-11 H11-55 H12-48 H11-24 H12-9 H12-4 H12-7 H12-15 H19-9 H8-45 H11-27 H9-63 H12-12 H12-33 H12-42 H11-33 H17-54 H9-37 H11-21 H9-6 H11-25 H19-7 H12-13 H19-4 H8-10 H8-42 H12-28 H12-65 H15-31 H17-1 H8-52 H12-5 H5-75 H11-17 H11-19 H12-29 H5-11 H5-74 H5-18 H5-21 H17-38 H8-50 H9-15 H8-46 H12-45 H17-64 H5-29 H19-1 H8-12 H11-5 H12-49 H19-47 H8-7 H12-14 H19-16 H5-33 H8-53 H9-19 H9-21 H5-54 H17-63 H8-15 H8-35 H5-41 H11-37 H11-40 H9-22 H11-38 H17-9 H17-19 H17-14 H17-24 H17-13 H17-21 H17-49 H17-52 H17-39 H17-48 H17-62 H9-38 H17-57 H17-28 H17-45 H15-44 H5-3 H5-23 H9-12 H8-28 H5-36 H5-35 H8-39 H15-6 H15-9 H5-61 H17-60 H5-66 H5-67 H17-68 H17-66 H5-48 H5-53 H15-33 H17-36 H5-28 H5-52 H8-22 H5-42 H9-17 H5-10 H8-30 H5-63 H5-72 H11-23 H9-32 H5-15 H17-40 H5-39 H15-32 H17-18 H5-43 H8-6 H5-65 H8-34 H8-36 H12-58 H19-5 H15-13 H9-23 H15-35 H19-19 H15-40 H15-42 H15-38 H19-58 H19-62 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 Average Distance Between Clusters
  84. 84. Are the parental performancescorrelated with the performances of their BC progenies?
  85. 85. Genetic background effects in introgression breeding
  86. 86. Submergence Tolerance Number of submergence tolerant plants in 9 BC2F2 and 3 BC3F2 populations under the field conditionVG Donors Origin TKM9 (SS) Khazar (SS) FR13A (T) Total (I) (I) (J)I IR64 (S) India 12 8 14 34I Teqing (SS) India 10 9 8 27 NPT (SS)J Iran 6 6 6 18 BC2F2 NPT (SS)J Iran 10 71 2 83 BC3F2 Total 38 94 30 162
  87. 87. Yield responses of the 193 parental lines of IRMBP to the terminal drought under the lowland condition25 ± -19.1±44.0%20151050 -100 -80 -60 -40 -20 0 20 40 60 80 100 120 140 160 Yield reduction (in %)
  88. 88. Summary of selected drought tolerant BC2F2 plants under lowland stress conditions NPT IR64 Teqing TotalTotal plants selected 897 2775 489 4161 # of selected plants 8.5 22.4 6.3 13.2 per population (3.8%) (10.0%) (3.0%) (6.8%) Range 0 - 85 0 - 100 0 - 30 0 - 100 No. of populations 113 124 105 320 No. of I donors 59 67 59 185 No. of J donors 32 45 19 96Contributing donors (%) 80.5 90.3 74.3 87.8
  89. 89. Parental performance and 442 selected DT BC2F2plants for drought tolerance from 19 BC populationsVG Donors Origin IR64 (S) Teqing (M) NPT(SS) Total LL (UL) LL (UL) LL I BR24 (MR) Bangladesh 14 (27) 12 (7) 3 29 (34) I STYH (S) Myanmar 20 (26) - 4 24 (26) I OM1723 (S) Vietnam 7 (17) 7 (6) 0 14 (23) J FR13A (SS) India 15 (16) 17 (15) 0 32 (31) J Type3 (S) India 23 (15) 10 (12) 0 33 (27) J Binam (M) Iran 20 (19) 14 (13) 1 35 (32) J HAN (M) China 11 (13) - 3 14 (13) I Zihui100 (S) China 8 - 9 17 J Khazar (MR) Iran 58 - 58 Total 176 (133) 60 (53) 22 256 (186)
  90. 90. Comparison of different IR64 and NPT BC generationsin screening for anaerobic germination (%) BC2F2 bulks BC3F2 bulks BC4F2 bulks IR64 NPT IR64 NPT IR64 NPT Total number of populations 9 10 - 10 9 10 Surviving plants/population 0 – 28 0 - 50 - 33 - 78 17 - 78 97 - 162 Number of indica donors 7 8 - 8 7 8 Selected lines (indica) 36 158 - 452 296 1038 Selection intensity (%) 5.1 19.8 - 28.3 21.1 64.9 Number of japonica donors 2 2 - 2 2 2 Selected lines (japonica) 2 8 - 35 44 121 Selection intensity (%) 2.0 8.0 - 17.5 22.0 60.5 Mean selection intensity (%) 4.4 13.9 26.1 21.3 62.7BC2F2, BC3F2 and BC4F2 bulks all had 200 seeds in 2 replications. For individual BC populations of200 plants, a difference of 4% between two populations in selection intensity (survival rate) isstatistically significant at P < 0.05 when the selection intensity is between 0.1 and 0.5.
  91. 91. Screening for seedling cold toleranceTwelve-day old seedlings were subjected to cold temperature for18 days at the mean daily temperature of 11.8 Co, including 3-dayof low temperature at 8 Co between April 24-26 (LAAS, 2002).
  92. 92. Seedling Cold Tolerance (from NARES)Selection of 861 C418 plants with seedling cold tolerance from 28 C418 BC2F2 populations 2002 (LAAS) Non-CT BC2F2 CT donors donors # of populations 28 2 26 # of surviving plants 10.3% 14% 0.3 per population Range 1.4 – 19.3% 10 – 16% 0 – 3.0% # of surviving plants 10.3% 7.6% 10.5% per BC populationThe mean population size was 310, ranging from 196 – 465, therecipient, C418 (japonica) was killed by the stress.
  93. 93. Genetic background effects on the performance of BC progeniesTeqing / Chipda NPT / Chipda
  94. 94. Donor and recipient effects on the number of BC2F2 plantsselected under lowland drought during the 2002 dry season Donor Recurrent parent Donor Recurrent parent IR64 Teqing NPT IR64 Teqing NPT ASD 16 10*** 0 Moroberekan 13 11 ASD18 59*** 0 54*** MR 77 31**** 0 B4122 37*** 2 1 Palung 2 33 36 Budda 75*** 11 Pokhreli 119**** 7 30*** Chipda 47*** 0 85**** Pusa 15** 4 Chorofa 1 20*** Rasi 63*** 9 Dacca 6 20 19 Rusty Late 38**** 2 4 Dhan4 1 0 Sadajira 19 55**** 0 Doddi 81*** 2 Shwewartun 5* 0 6** Gajale 61*** 22 SLG-1 26**** 0 Giza 14 29*** 4 SML242 6** 0 5*
  95. 95. Genetic background effects on the number of survival plants under submergence in 33 BC4F2 populations from crosses between 3 RPs and 11 donors Cross Survival (%) Z value Cross Survival(%) Z value IR64/SN89366 3.33 1.87 NPT/C418 0.00 Teqing/SN89366 6.67 3.75 IR64/CH448 9.33 4.14 NPT/SN89366 0.00 Teqing/CH448 7.33 3.25 IR64/Y134 7.33 3.45 NPT/CH448 0.00 Teqing/Y134 7.33 3.45 IR64/FR13A 7.67 3.64 NPT/Y134 0.00 Teqing/FR13A 6.67 3.17 IR64/BR24 8.00 3.61 NPT/FR13A 0.00 Teqing/BR24 8.00 3.61 IR64/Madhukar 7.33 3.60 NPT/BR24 0.00 Teqing/Madhukar 6.00 2.95 IR64/Zihui 100 11.67 4.87 NPT/Madhukar 0.00 Teqing/Zihui 100 7.33 3.06 IR64/IR50 6.67 3.13 NPT/Zihui 100 0.00 Teqing/IR50 8.00 3.76 IR64/IR72 8.00 0.45 NPT/IR50 0.00 Teqing/IR72 8.00 0.45 IR64/Jhona349 5.00 2.73 NPT/IR72 7.00 Teqing/Jhona349 5.67 3.09 IR64/C418 7.33 3.19 NPT/Jhona349 0.00 Teqing/C418 10.00 4.35
  96. 96. Genetic background effects on the number of survival plants under submergence in 33 BC4F2 populations from crosses between 3 RPs and 11 donors Cross Survival (%) Z value Cross Survival(%) Z value IR64/SN89366 3.33 1.87 NPT/C418 0.00 Teqing/SN89366 6.67 3.75 IR64/CH448 9.33 4.14 NPT/SN89366 0.00 Teqing/CH448 7.33 3.25 IR64/Y134 7.33 3.45 NPT/CH448 0.00 Teqing/Y134 7.33 3.45 IR64/FR13A 7.67 3.64 NPT/Y134 0.00 Teqing/FR13A 6.67 3.17 IR64/BR24 8.00 3.61 NPT/FR13A 0.00 Teqing/BR24 8.00 3.61 IR64/Madhukar 7.33 3.60 NPT/BR24 0.00 Teqing/Madhukar 6.00 2.95 IR64/Zihui 100 11.67 4.87 NPT/Madhukar 0.00 Teqing/Zihui 100 7.33 3.06 IR64/IR50 6.67 3.13 NPT/Zihui 100 0.00 Teqing/IR50 8.00 3.76 IR64/IR72 8.00 0.45 NPT/IR50 0.00 Teqing/IR72 8.00 0.45 IR64/Jhona349 5.00 2.73 NPT/IR72 7.00 Teqing/Jhona349 5.67 3.09 IR64/C418 7.33 3.19 NPT/Jhona349 0.00 Teqing/C418 10.00 4.35
  97. 97. Can we develop ILs with extreme phenotypes for selected target traits?
  98. 98. Screening results of 11 BC2F4 backcross populations derived from crosses between a japonica variety, Chaoyou 1 (the recurrent parent) and 11 donors for cold tolerance at the booting stage and for heat tolerance at the flowering stage Selection for heat tolerance at the flowering stage Selection for cold tolerance at the booting stage Seed set (%) Spikelets per panicle Seed set (%) Donor 1 N SI (%) 2 Mean 3 Range N SI (%) Mean 3 Range Mean 3 Range Bg90-2 (I) 41 9.11 63.3 d 50.3 - 86.5 25 6.25 41.3 abc 23.0–77.0 171.2 abc 124.0–253.1 9 2.25 38.1 abcd 19.5–50.0 192.5 ab 143.3–275.5 X21 (I) 29 6.44 64.3 cd 50.6 - 87.1 X22 (I) 28 6.22 65.6 bcd 50.7 - 87.3 - - - - - - Q5 (I) 31 6.89 71.1 abc 50.9 - 91.4 6 1.50 41.1 abc 19.9–75.4 160.4–274.2Chhomrong (J) 24 5.33 51.4 - 87.8 17 4.25 37.7 abcd 19.3–65.5 172.9 abc 115.9–258.8 Doddi (I) 25 5.56 71.0 abc 50.2 - 90.0 - - - - - -Feng-Ai-Zhan (I) 44 9.78 52.2 - 98.5 12 3.00 31.3–70.1 180.7 abc 138.2–238.0 9 2.25 28.9 d 17.0–44.4 171.5 abc 112.0–216.7Shennong265 (J) 21 4.67 69.2 abcd 50.7 - 93.8 25 6.25 45.5 ab 23.9–65.6 83.2–255.4 Yuangeng7 (J) 41 9.11 71.1 abc 50.0 - 90.1 13 3.25 33.0 cd 17.0–48.9 171.9 abc 111.6–230.4 OM997 (I) 21 4.67 72.1 ab 54.9 - 89.6 8 2.00 33.6 abcd 24.9–48.3 175.5 abc 121.4–280.4 Cs94 (I) 19 4.22 64.2 cd 51.4 - 86.0 124 3.44 5.2 e 0.0–7.9 157.4 bc 127.4–178.6 Chaoyou (J) 324 6.55 24.8 e 19.0 - 30.0 2N is the number of cold tolerant or heat tolerant BC plants selected from each population and SI = selection intensity. 3 Different letters indicate the statistical significance in seed set at P < 0.05, based on the Duncan testing of ANOVA.
  99. 99. Table 6 Performances for AG of 11 promising BC4F3 lines and their donors Recipient Donor Seedling height (cm) AG (%) Emerging at 10 d (%) NPT Khazar 33.5 90.0* 20.0 NPT Khazar 32.5 95.0** 75.0** NPT FR13A 37.7 95.0** 30.0 NPT TKM 9 37.7 100.0*** 95.0*** NPT TKM 9 36.2 100.0*** 60.0* NPT TKM 9 37.9 100.0*** 95.0*** NPT Babaomi 34.9 100.0*** 50.0 NPT Babaomi 36.7 100.0*** 50.0 NPT OM1706 33.9 100.0*** 65.0* NPT OM1706 36.1 100.0*** 80.0*** TKM 9 I 31.4 20.0 12.7 Khazar J 30.3 3.0 0.0 Babaomi I 26.3 5.0 0.0 Jiangxi-Si-Miao I 31.5 9.0 0.0 OM1706 I 29.1 18.0 2.0 IR64 I 26.5 20.0 2.0 NPT J 36.2 68.0 39.0I = indica and J = japonica. Traits were measured at 21 d after seeding. All 10 ILs had significantly higher AG than therecurrent parent, NPT at P < 0.001.
  100. 100. Trait specific introgression lines developed # of BC2F2 No. of selected Target traits populations BC2F3 lines Drought tolerance 350 4687 BPH resistance 203 522 Salinity tolerance 203 1022Anaerobic germination 130 368 Zinc deficiency 129 1211Submergence tolerance 264 798 Grain quality 65 580 Other traits 375 12,000+ Total 20,000+
  101. 101. Summary of Selection Experiments• Most donors contributed performance enhancing alleles to their BC progenies regardless of their performances;• Appropriate screening (selection) is the key to identify improved target traits in the BC progenies;• More distantly related donors, particularly landraces, tend to give more transgressive segregations for abiotic tolerance in the BC progenies.
  102. 102. ConclusionsThere are tremendous amounts of hidden geneticdiversity in the current rice germplasmcollections for genetic improvement of all targettraits we tried, which have not been exploited;Selection of parental lines for breeding based onphenotype practiced by most breeders is a poorway in exploiting novel genetic variation forcomplex traits;Backcross breeding, effective selection (efficientscreening) combined with DNA markers are theeffective way to exploit this hidden diversity;
  103. 103. What are we going to do with this large number of ILs?1. Direct development of new cultivars;2. As genetic stocks for discovery of DT alleles or QTLs and functional genomics of DT;3. As parents for development of superior rice cultivars by QTL pyramiding

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