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.

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

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2012 GSR - breeding technology 2012 GSR - breeding technology Presentation Transcript

  • 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
  • SubjectsIntroductionConcept of GSRGSR Breeding Strategy andTechnologyPerspectives
  • 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
  • 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
  • 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
  • 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
  • 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
  • Annual yield losses~20% from abiotic stress: drought, problem soils, etc)~15% from biotic stress: diseasesand insects, even with the heavy uses of pesticides.
  • 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.
  • 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
  • Consequences of the Green Revolution Productivity Diversity
  • 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).
  • 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)
  • 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
  • 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 27% of modern varieties 90% of the 73% of Cultivated rice landraces Everson et al. 1998
  • 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
  • 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
  • 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
  • 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
  • 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 %)
  • 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)
  • 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!
  • 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
  • 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
  • The Basic IdeaFull Exploitation of The Genetic Diversity in the Primary Gene Pool of Rice
  • 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
  • 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, yield potential, andgrain quality for the major ricegrowing areas in China.
  • 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.
  • Proof of the Concept
  • 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)?
  • Part I: Introgression breeding and mass selectionRecurrent ParentsIR64 - Indica, high yield/widely adaptableNew Plant Type - Japonica, high yield potentialTeqing - Indica, high yield/widely adaptable
  • 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
  • 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
  • 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
  • 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)
  • 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%
  • 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
  • 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
  • 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
  • Selection strategy for target traits in random BC progenies
  • 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)
  • Variation in BC2F2 populations for drought tolerance under the lowland conditions
  • 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
  • The Screening of BC2F2 populations under upland drought conditions The RP, IR64
  • 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
  • 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)
  • 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
  • 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 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
  • 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.
  • 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
  • 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
  • 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 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
  • Screening for BPH Resistance IR64
  • 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.
  • 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.
  • 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 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
  • 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 (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
  • 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.
  • 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
  • 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.
  • 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
  • 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.
  • 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
  • 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 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 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
  • 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 %)
  • 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
  • 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)
  • 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.
  • 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).
  • 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.
  • 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 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*
  • 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
  • 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
  • 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 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.
  • 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.
  • 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+
  • 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.
  • 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;
  • 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
  • Progeny Testing of DT ILs Under Stress (no irrigation after transplanting) DT C418 ILs Check (C418)
  • Progeny Testing Under Stress(no irrigation after transplanting) Promising DT C418 ILs
  • 2001-2002 DS BC2F4 progeny testingIR64 ILs for quality IR64 (CK) DT IR64 ILs
  • Performance of two DT NPT ILs under severe stress DT NPT ILs NPT CK
  • Performance of some promising salinitytolerant IR64 ILs in the field condition in Iloilo (EC 18 dSm-1 ) 11/17, 2003
  • Performance of some promising salinitytolerant IR64 ILs in the field condition in Iloilo (EC 18 dSm-1 ) 11/17, 2003
  • Promising varietiesdeveloped in the BC breeding program
  • The Recurrent Parents C418 Liaojing454(restorer)
  • Preliminary Yield Trials of Promising DT/WUE ILs 30% water saving 70% 50% water water saving saving
  • Replicated Preliminary yield trial of DT/WUE ILs (Shengyang/2006.9)Completely Water rainfed saving 70%Water Watersaving saving 50% 30%
  • Promising DT/WUE 辽粳9号对照 辽粳 号对照 IL -HR95 抗旱导入系的节水实验
  • Yield performances of two promising DT/WUE ILs in replicated yield trials under stress and non-stress conditions (Shengyang/2006) 25Yield change over CK (%) 20 Normal irrigation 15 30% water saving 10 50% water saving 5 70% water saving 0 Completely rainfed -5 HR94 HR95 Liaojing 9 (CK) in Liaojing 454background
  • Yield potential and DT/WUE of DT ILs% changeover CK Rainfed 70% 50% 30% Normal 25 20 15 10 5 0 -5 -10 HR354 HR525 HR9 HR94 HR95 LJ9 (C418) (C418) (C418) (LJ454) (LJ454) (CK)
  • Promising DT/WUE FAZ ILsZhonghua 1 Zhonghua 2
  • GSR material ST in Infanta• GSR material• material (572 lines)• Other group’s material 2011-10-20 Lijun Meng
  • High EC Low EC GS NON-s R GSRea
  • NON GSR material GSR material
  • HHZ HHZ HHZ HHZ 23-Sal8-DT1-ST1
  • R1 R2HHZ 23-Sal24-DT1-STI HHZ 23-Sal24-DT1-STI HHZ 23-Sal8-DT1-ST1 HHZ 22-DT3-LI1-DT1
  • HHZ
  • CKNSIC Rc 222
  • 2011-10-7 HHZ 24-DT6-DT1- IR 63307-4B-4-3 HHZ 23-DT14-DT1-DT1 DT1
  • 2011-10-7 HHZ 25-SAL9-Y3-ST1
  • Introgression Breeding for improving 2 or more complex traits
  • RP X Donors BC2F1 X BC2F2Screening under Screening under Screening under Selection for high yield severe salinity submergence severe drought under normal condition ST ILs SUBT ILs DT ILs HY ILsPT under severe PT under PT under severe PT for high yield under salinity submergence drought normal condition Promising ILs with more than one target traits to be tested in multi-location yield trials in target Es
  • An example of the modifiedintrogression breeding procedure used in GSR development - Development of HHZ ILs with one ormore improved target traits (yield, DT, ST,SUBT and performance under low inputs)
  • Huang-Hua-Zhan (HHZ) is a mega rice variety with high yield potential, superior quality currently grown in ~2 million ha in South and central China. It has wide adaptability (yieldedsignificantly higher than the best local checks) at > 17 testing sites of Asia and Africa Mozambique Cote D’ivoir Bangladesh Philippines Indonesia Tanzania Pakistan Vietnam Rwanda Nigeria Mali AllHHZ 2 1 3 1 3 1 2 1 1 1 1 17
  • Two batches of 16 populations with HHZ as the recipient and 16 donors from 9 different countries Batch Pop. Donor Country of origin Gen.(10 DS) 1 HHZ5 OM1723 Vietnam (I) BC1F5 1 HHZ8 Phalguna India (I) BC1F5 1 HHZ9 IR50 IRRI (I) BC1F5 1 HHZ11 IR64 IRRI (I) BC1F5 1 HHZ12 Teqing China (I) BC1F5 1 HHZ15 PSB Rc66 Philippines (I) BC1F5 1 HHZ17 CDR22 India (I) BC1F5 1 HHZ19 PSB Rc28 Philippines (I) BC1F5 2 HHZ1 Yue-Xiang-Zhan China (I) BC1F4 2 HHZ2 Khazar Iran (J) BC1F4 2 HHZ3 OM1706 Vietnam (I) BC1F4 2 HHZ6 IRAT352 CIAT (upland) BC1F4 2 HHZ10 Zhong 413 China (I) BC1F4 2 HHZ14 R644 China (I) BC1F4 2 HHZ16 IR58025B IRRI (I) BC1F4 2 HHZ18 Bg304 Sri Lanka (I) BC1F4
  • The Introgression Breeding Procedure 06WS First batch of 8 HHZ BC1F2 populations (08WS) 08WS Yield traits DT screen ST screen SUB screen Random plants1st roundselection 82 HY plants 109 DT plants 120 ST plants 3 SUBT plants QTL/Allelic 311 genotyped/progeny tested for all target traits diversity discovery 09DS 212 Yield 153 DT screen 211 ST screen 171 SUB screen for target 2nd round traits selection 09WS 495 genotyped/progeny tested for all target traits3rd roundselection Confirming genetic 10DS 12 RYT and 108 PYT under DT, low input, NC networks for target traits and their genetic relationships 68 promising ILs Used as parents for designed QTL 68 replicated 2 NCT10WS/11DS 3 Demo pyramiding yield trials in 11WS
  • The Introgression Breeding Procedure06WS Second batch of 8 HHZ BC1F2 populations (09WS)08WS Yield traits DT screen ST screen SUB screen Random plants 119 HY plants 210 DT plants 314 ST plants 21 SUBT plants QTL/Allelic 664 genotyped/progeny tested for all target traits diversity discovery for target10DS Yield under DT screen ST screen SUB screen NC & LI traits 491 HY&FUE ILs 176 DT ILs 44 ST ILs 221 SUB ILs Confirming genetic10WS 865 genotyped/progeny tested for all target traits networks for target traits and their 232 yield genetic relationships 130 DT screen ST screen SUB screen11DS under NC&LI 305 HY&FUE ILs 570 DT ILs ST ILs SUB ILs RYT & Promising ILs as parents for11WS DEMO PYT designed QTL pyramiding
  • HHZ ILs with one or more improved target traits selected from the 8 2nd BC populations Improved traits Selected ILs PYT NCYT DT+LI 210 24 8 DT+ST 58 13 5 DT+SUBT 24 14 DT+HY 28 28 16 LI+ST 0 0 1 LI+HY 25 2 ST+SUBT 1 9 ST+HY 33 33 8 SUBT+HY 7 2 1 DT+ST+SUBT 35 3 1 DT+ST+HY 154 9 DT+SUBT+HY 58 3 LI+ST+SUBT 20 LI+ST+HY 117 LI+SUBT+HY 36 ST+SUBT+HY 39 Total 845 140 40
  • Trait specific HHZ ILs developed in CAAS and IRRI in 4 years Number ofTraits Institution ILs selected donors CAAS 8 180Drought tolerance IRRI 15 978 CAAS 40 1200Salt tolerance IRRI 15 633Tolerance to low inputs IRRI 250 350Submergence tolerance IRRI 4 121 CAAS 8 210High yield IRRI 15 610High yield under low IRRI 451 451inputs CAAS 40 1809Total IRRI 15 1260
  • Performances of some high yield HHZ ILs under irrigated conditions at IRRI Grain Yield (t/ha) Mean % over Designation over % over NSICRc1 2010WS 2011DS seasons IR72 58HHZ8-SAL6-SAL3-Y2 6.55ab 8.0ab 7.28 10.56 12.27Mestizo7 (Hybrid) 5.68 bcde 8.7a 7.19 9.27 10.96HHZ12-DT10-SAL1-DT1 6.75a 7.2 bcde 6.98 6.00 7.64HHZ5-SAL10-DT1-DT1 6.14abcd 7.4 bcd 6.77 2.89 4.48IR72 5.96abcde 7.2 cde 6.58 0.00 1.54NSICRc158 5.86 bcde 7.1 cdef 6.48 -1.52 0.00 Reason: Higher HI, spikelets per panicle;panicles per sqm;total spikelets per sqm,CGR Plot size: 30 sqm under SSNM
  • DT HHZ5-Sal14-Sal2-Y2 APO (check)
  • The HHZ ILs in RYT have diverse grain pasting properties suitable for consumers with different taste preferences 1 2 6000 120 3 4 5 6 5000 100 7 8 9 10 4000 11 12 80 13 14Viscosity, cP Temperature 3000 15 16 60 17 18 2000 19 20 21 22 40 1000 23 24 25 26 20 27 28 0 0 100 200 300 400 500 600 700 800 29 30 31 32 -1000 0 Tim e, sec 33 34 35 36 AC=14.5-31.6%; GT= H-I-L; Protein=7.8-11.2%
  • Development of ILs with resistances to multiple abiotic/biotic stresses BC2F2Bulk populations Screen for the Drought screen – DT ILs Genotypingprimary target trait Screen for Yield related Disease and QTL & QTL other traits Salinity traits insect resistances networks for target and non- target traits Promising ILs with multiple desirable traits (QTLs) Parents for DQP Promising lines Breeding by Yield trials at DQP procedures multiple locations
  • Development of IR64 ILs with multiple desirable traitsIR# RP(%) Donor BPHR SBR ST SUB Yield/plant (g) (Score) (LL, cm) (Score) (%) Mean CK%IR82853-18 84.4 Type 3 3.2 3.0 25.7 68.6IR82853-30 84.2 Type 3 3.0 3.8 27.2 77.9IR82908-5 75.8 Bg300 3.0 4.0 17.9 17.1IR82907-18 89.1 Babaomi 3.0 3.7 - -IR82855-26 81.0 Binam 3.0 4.0 26.7 74.8IR82861-10 80.5 RF13A 3.0 4.0 17.4 13.6IR82865-2 89.5 Haonnong 3.0 3.0 15.9 3.9IR82859-24 88.6 OM1723 3.0 4.0 20.7 35.3IR82940-7 84.3 Basmati 3.0 100.0 - -IR82863-2 79.5 Zihui 100 3.0 100.0 26.0 70.3IR82855-1 91.7 Binam 3.0 3.0 22.1 44.7IR82859-13 97.1 OM 1723 3.6 4.0 17.7 15.8IR82865-24 89.5 Haonnong 3.0 4.0 88.9 34.5 125.8IR82861-28 81.4 FR13A 3.0 4.0 100.0 - -IR64(CK) 100.0 15.3 -
  • Question:• When we are trying to improve more than one complex trait, what trait(s) should be selected first, yield or abiotic/biotic stresses?
  • HHZ x Donors (1=IR64 , 2=AT354 , 3=C418) Population F1 x HHZ development and 25 BC1F1 x HHZ selection 25 BC2F1 X 3 bulk BC2F2s (480) 2010 Beijing Summer 1: DT (19) 1: HY (26) 1: ST (57) 2: DT (29) 2: HY (28) 2: ST (49) BC2F3s1st selection 3: DT (33) 3: HY (29) 3: ST (56) 2010 Beijing Summer 2010 Hainan Winter 2010 Winter phytotron 1: HY (0) 1: DT (12) 1: HY (2) 1: DT (0) 1: ST (25)2st selection BC2F4s 2: HY (2) 2: DT (23) 2: HY (1) 2: DT (0) 2: ST (28) 3: HY (3) 3: DT (8) 3: HY (2) 3: DT (1) 3: ST (29) 2010 Hainan Winter 2010 Hainan Winter 1: HY (0) 1: DT (0) 1: DT (3) 1: HY (3) 2: HY (2) 2: DT (0) 2: DT (4) 2: HY (5) BC2F5s3nd selection 3: HY (1) 3: DT (2) 3: DT (2) 3: HY (2)
  • Performances of 83 HHZ BC2F5 introgression lines selected for high yield and their RP (HHZ) under drought stress (S) and normal (N) conditions of Hainan in 2010 (1N: number of HY ILs, T: treatment, N: normal condition, S: drought stress condition,)Donor 1N T HD PH FGN TGW SNP SF PN GY N Mean 23.4±0.6 175.4±16.1 192.0±18.3 90.7±1.8 8.3±1.2 22.0±1.3HHZ 116.2±3.2 75.6±1.4(RP) S Mean 21.0±0.4 137.1±13.7 154.4±14.2 86.4±2.0 8.8±1.2 17.6±0.7 107.3±11.5 74..0±1.6 Mean 22.5±3.0 171.9±47.6 197.3±49.3 86.8±5.5 7.9±1.6 22.7±6.6 111.8±5.1 75.6±4.4 N Range 15.2-26.0 106.7-255.8 136.3-272.4 74.4-93.8 6.2-10.6 12.8-32.6 101.0-111.0 66.3-78.9IR64 26 Mean 20.2±1.8 135.1±31.8 154.3±30.2 74.3±11.2 9.2±2.3 ± 14.8±5.2 91.3±5.2 71.3±4.7 S Range 17.5-22.6 80.2-194. 9 98.1-203.6 49.4-91. 4.4-14.3 4.3-23.9 78.0-99.5 65.0-77. 5 Mean 20.3±1.0 184.8±28.8 231.0±31.4 79.9±4.3 10.2±1.6 27.6±5.5 107.1±7.3 72.5±2.3 N Range 19.0-22.0 127.8-217.8 166.7-273. 1 72.7-85.7 8.7-12.3 19.3-35.0AT354 28 98.5-110 69.2-74.8 Mean 18.6±1.2 119.1±19.7 145.3±26.4 63.3±13.4 9.6±1.9 ± 10.9±3.6 90.1±7.0 65.7±3.9 S Range 17.1-20.5 73.4-156.1 101.6-176.5 51.1-80.2 7.3-12.5 6.9-19.1 82.0-99.0 58.5-68.9 Mean 23.2±1.7 192.1±36.3 217.2±40.0 88.4±5.3 7.8±1.5 24.4±5.7 111.6±4.3 76.2±3.7 N Range 20.6-26.1 99.7-228. 7 142.4±270.6 70.4-92.5 4.6-11.7 13.9-40.4C418 29 99.5-117.5 76.4-81.2 Mean 20.8±1.5 143.6±28.8 155.4±24.4 79.2±12.1 9.2±1.6 18.7±5.9 97.7±5.7 75.4±5.5 S Range 18.0-23.0 87.1-175.7 114.2-197.3 55.6-89.7 7.2-11.8 7.6-26.5 86.5-103 69.7-80.4
  • The numbers of ILs selected for high yield from the 3 populations that deviatedsignificantly HHZ for 9 measured traits evaluated under drought stress (S) and normal(N) conditions of Hainan in 2010 HD PH GW FGW SNP SF PN GY Donor T N1 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 N1 N2 IR 26 0 5 0 2 1 4 1 1 1 0 0 6 0 0 2 0 AT354 N 16 0 9 0 1 0 12 0 1 1 0 0 12 3 0 1 0 C418 22 0 3 0 0 0 2 0 1 1 0 0 1 1 1 2 0 IR 26 0 25 2 5 0 5 0 5 0 1 0 6 0 2 0 2 AT354 S 16 0 16 0 15 0 6 0 9 0 0 0 13 1 0 0 7 C418 22 0 15 2 0 0 1 0 1 0 0 0 1 0 0 1 1N1 is the total number of selections based on grain yield (GY) per plant in BC2F5 populations. N1 and N2 are thenumbers of the BC2F5 lines showing significantly higher or significantly lower than HHZ for the measured traits.HD = heading date, PH = plant height, PL = panicle length, GW = 1000-grain weight, FGN = filled grain numberper panicle, SNP = spikelet number per panicle, SF = spikelet fertility, PN = panicle number per plant, GY =grain yield.
  • Performances of some promising DT ILs under drought stress and normal conditions in Beijing and Hainan, 2010 Under the normal condition Under the drought stress conditionL Donor Line# TG HD PH TGW FGN SNP SF PN GY HD PH FGN SNP SF PN GY W HHZ 115.3 - 23.1 172.8 189.0 91.4 7.6 23.1 - - - - - - - - WT111 106.0 - 20.4 227.9 260.4 87.5 9.3 39.2 104.0 - 18.6 135.4 142.5 94.7 4.3 8.8 WT115 107.0 - 20.4 208.4 228.5 91.1 8.3 31.6 109.5 - 19.2 106.1 148.7 71.3 3.0 4.5 AT354 WT91 101.0 - 18.9 171.4 210.4 81.5 7.0 23.9 104.0 - 16.1 112.6 132.9 85.0 5.5 5.5BJ WT97 106.5 22.7 144.2 175.2 82.3 6.7 24.9 110.5 19.6 119.6 152.2 78.5 4.0 6.5 WT183 103.5 - 21.0 251.7 300.7 83.7 8.3 33.5 113.5 - 17.5 123.9 151.2 81.9 5.3 5.9 WT184 107.0 - 20.9 187.7 204.7 91.7 8.3 31.6 113.0 - 17.8 117.6 149.6 78.6 5.3 6.0 C418 WT185 103.5 - 21.8 165.6 189.9 87.2 10.7 32.5 115.5 - 19.2 141.7 159.0 89.1 4.0 8.2 WT180 105.0 - 18.8 215.6 240.6 89.6 8.0 23.9 116.0 - 16.8 127.2 199.5 63.7 5.5 4.4 HHZ 116.2 75.6 23.4 175.4 192 90.7 8.3 22.0 107.3 74 21.0 137.1 154.4 86.4 8.8 17.6 WT111 105.0 68.0 22.3 162.8 189.4 86.0 7.3 19.5 111.0 65.3 19.3 95.8 140.2 68.6 9.0 14.5 10. WT115 108.0 73.8 22.0 164 195.3 83.9 8.0 20.6 115.5 75.3 20.2 111.1 155.7 71.3 16.4 4 AT354 11. WT91 111.0 80.7 20.9 181.8 232.1 78.3 11.5 38.3 119.5 73.5 17.9 123.4 144.9 85.8 21.6 6HN WT97 109.0 77.2 21.2 274.3 318.7 86.0 8.5 32.3 114.0 68.1 20.8 104.2 161.0 64.9 9.6 17.9 WT183 114.5 76.5 23.8 133.8 145.0 92.3 6.7 22.5 125.0 74.6 20.8 92.9 111.5 83.2 9.9 23.9 WT184 114.0 74.4 24.7 156.3 176.7 88.5 8.6 29.3 125.0 75.6 20.8 123.6 140.6 89.0 6.8 15.5 C418 WT185 113.0 73.3 24.5 174.6 192.2 91.1 9.8 31.3 121.0 72.8 21.4 119.3 132.3 90.2 9.4 26.9 WT180 115.0 81.2 24.5 188.4 200.8 93.8 8.8 36.2 125.0 85 21.9 150.4 183.6 82.1 8.7 26.9
  • The selection order of DT(1) – HY(2) wasmore effective than that of HY(1) – DT(2)to combine both HY and DT;This result can not be adequatelyexplained by the current quantitativegenetics theory. However, it does indicatethat it will make differences to determinethe correct order of target traits to beselected when multiple complex traits areto be improved.
  • 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
  • Uses of ILs for pyramiding genes/traitsfrom 2 or more donors to develop GSR varieties
  • Experimental design for simultaneous improvement of DT, ST and yield potential by pyramiding IL1(HY, DT) x IL2(HY, DT) IL3(HY, ST) x IL4(HY, ST) F2 F2Screen Screen Select for Screen Screen Select forfor DT for ST HY and for DT for ST HY and random random DT ST DT STPDLs PDLs PDLs PDLs Genotyping and progeny Genotyping and progeny testing for all target traits testing for all target traits HY, DT, ST HY, DT, STPDLs (PDL1) Discovering genetic networks for HY, DT, PDLs (PDL2) ST and their genetic overlap
  • Designed QTL pyramiding based on the genetic and phenotypic information of parental ILs IR64/BR24//IR64///IR64 IR64/Binam//IR64///IR64 BC2F2 BC2F2 Screening under drought Genotyping X Genotyping DT IR64/BR24 IL DT IR64/Binam IL and QTL and QTLidentification identification F1 X F2 Screening under severe drought Progeny testing Survival plants Genotyping
  • Pyramiding F2 population screened undersevere lowland drought at the reproductive stage (2002-03 DS) IL1 F2 IL2
  • An average of 25% of the progeny of the 9 F2 populations survived the severe drought stress P1 IL P2 IL F2 populationCross Line Donor Line Donor Size No. SI (%) II-1 DGI-74 BR24 DGI-187 Binam 318 90 28.3 II-2 DGI-21 STYH DGI-62 BR24 190 55 28.9 II-3 DGI-76 BR24 DGI-238 OM1723 248 55 22.2 II-4 DGI-21 STYH DGI-60 BR24 137 25 18.2 II-5 DGI-29 STYH DGI-353 Zihui100 154 30 19.5 II-6 DGI-75 BR24 DGI-187 Binam 154 30 19.5 II-7 DGI-142 Type3 DGI-373 HAN 255 70 27.5 II-8 DGI-146 Type3 DGI-353 Zihui100 135 70 51.9 II-9 DGI-150 Type3 DGI-374 HAN 219 30 13.7Total 1810 455 25.1
  • Yield performances of 90 (3 major group genotypes) PLs from pyramiding population 1 in 2004 dry-season8.0 Control 2.0 Terminal stress6.0 1.6 1.24.0 0.82.0 0.4 0 0 GG1 GG2 GG4 GG3 IR64 GG1 GG2 GG4 GG3 IR64 ± GG1 (X = 109±20, 66%) ± GG1 (X = 35±8, 361%) ± GG2 (X = 247±35, 149%) ± GG2 (X = 33±12, 344%) ± GG4 (X = 117±18, 70%) ± GG4 (X = 34±8, 373%) ± GG3 (X = 140±33, 84%) ± GG3 (X = 35±13, 364%) ± IR64 (X=166±10, 100%) ± IR64 (X=9.7±5, 100%)
  • ANOVA Result for Yield of 2004 Dry SeasonYieldSource DF MS F P>F R2 (%)Stress 1 824575.5 820.64 0.0001 23.2Group 5 90892.7 90.46 0.0001 12.8Group(Line) 83 1778.9 1.77 0.0002 4.1Stress*Group 5 97151.2 96.69 0.0001 13.7Stress*Group(Line) 83 1576.9 1.57 0.0029 3.7StressGroup 5 312.9 1.17 0.3255 2.0Group(Line) 83 374.6 1.4 0.0332 40.0ControlGroup 5 187440.6 113.55 0.0001 62.3Group(Line) 83 3086.6 1.87 0.0003 17.0
  • Yield performances of the 4 group genotypes under the rainfed upland stress and non-stress conditions in 2004 wet-season Control Stress500 160 140400 120300 100 80200 60100 40 20 0 0 GG1 GG2 GG3 GG4 IR64 GG1 GG2 GG3 GG4 IR64 ± GG1 (X=124±20, 51%) ± GG1 (X=50±22, 1111%) ± GG2 (X=310±34, 129%) ± GG2 (X=44±24, 978%) ± GG4 (X=122±44, 51%) ± GG4 (X=62±31, 1378%) ± GG3 (X=212±37, 88%) ± GG3 (X=55±19, 1222%) ± IR64 (X=241±27, 100%) ± IR64 (X=4.5±8, 100%)
  • ANOVA Results for Yield of 2004 Wet SeasonYIELDSource DF MS F P>F R2(%)Stress 1 2491548.9 1676.0 0.0001 40.4Group 3 219664.3 147.8 0.0001 10.7Group(Line) 83 3057.4 2.06 0.0001 4.1Stress*Group 3 259596.4 174.6 0.0001 12.6Stress*Group(Line) 83 4307.3 2.9 0.0001 5.8StressGroup 3 5626.6 4.26 0.0011 6.9Group(Line) 83 1773.4 1.34 0.0527 36.3ControlGroup 3 464372.9 292.2 0.0001 65.3Group(Line) 83 5591.6 3.52 0.0001 21.8
  • Yield performance of the 4 group genotypes under mild stress in 2005 dry-season Stress Control8.06.04.02.0 0 GG1 GG2 GG4 GG3 CK GG1 GG2 GG4 GG3 CK ± GG1 (X=237±58, 149%) 151% ± GG1 (X=157±29, 75%) ± GG2 (X=313±46, 197%) 127% ± GG2 (X=247±33, 119%) ± GG4 (X=227±47, 143%) 131% ± GG4 (X=173±38, 83%) ± GG3 (X=249±50, 157%) 152% ± GG3 (X=164±28, 79%) ± IR64 (X=159±40, 100%) 76% ± IR64 (X=208±57, 100%)
  • Summarized Results from 1st round pyramiding breedingStrong selection under severe drought resulted ina few major group genotypes that havesignificantly improved DT, and showed highlysignificant differences in multiple phenotypesunder the non-stress conditions;We have identified a group genotype that havesignificantly improved yield potential andWUE/DT.
  • Summary1. Large numbers of loci are involved in DT of rice, and these DT loci appear to be under strong epigenetic control and tend to form complex genetic networks with clear hierarchy;2. Strong selection under severe drought resulted in a few major group genotypes that have significantly improved DT, and showed highly significant differences in multiple phenotypes under the non-stress conditions;3. Group 4 loci were associated with severe yield penalty by 30-50%;4. Group 5 loci were associated with improved yield potential (faster growth rate and greater sink capacity)5. We have identified promising rice lines with group genotype (1, 2, 3, and 5) that have significantly improved yield potential and WUE/DT. These lines are being tested in the multi-location yield trials in South/Southeast Asia.
  • Summarized results• The overall level of DT in rice appears to depend more on the combination of QTLs and less on the absolute number of QTLs that remains to be elucidated; and• High level of DT at the reproductive stage in rice is not necessarily associated with a penalty in yield potential under normal irrigated conditions. Thus, it is possible to combine high level of DT (at least for DT at the reproductive stage) and high yield potential.
  • Selection intensity of the 2nd round pyramiding F2 populations P1 PLs P2 PLs F2 Cross Line Origin Line Origin N Drought SI% III-1 DK47 II-1 DK109 II-2 420 56 13.3 III-2 DK47 II-1 DK148 II-2 428 60 14.0 III-3 DK47 II-1 DK158 II-2 439 97 22.1 III-4 DK47 II-1 DK356 II-3 413 72 17.4 III-5 DK47 II-1 DK388 II-3 425 49 11.5 III-6 DK39 II-1 DK148 II-2 75 24 32.0 III-7 DK39 II-1 DK158 II-2 422 70 16.6 III-8 DK39 II-1 DK356 II-3 269 55 20.4 III-9 DK39 II-1 DK388 II-3 435 20 4.6 III-10 DK65 II-1 DK109 II-2 382 50 13.1 III-11 DK65 II-1 DK148 II-2 305 40 13.1 III-12 DK65 II-1 DK158 II-2 403 51 12.7 III-13 DK65 II-1 DK356 II-3 112 20 17.9 III-14 DK65 II-1 DK388 II-3 220 3 1.4 Total 4748 667 15.0
  • Selection for HY and DT in 14 2nd DQP F2 populations fromcrosses bet. 8 IR64 PDLs each with multiple DT QTLs from 2 donors (05-06 DS, IRRI) Non-stress Stress Donor1 Donor2 Donor3 Donor4 Pop. size Sel. for yield Pop. size Sel. for DTSTYH BR24 BR24 Binam 127 8 (26.7) 75 24 (6.2)STYH BR24 BR24 Binam 450 21 (27.2) 422 70 (7.4)STYH BR24 BR24 OM1723 296 25 (26.4) 269 55 (6.6)STYH BR24 BR24 OM1723 405 20 (22.3) 435 20 (4.5)STYH BR24 BR24 Binam 450 30 (30.3) 420 56 (9.9)STYH BR24 BR24 Binam 435 17 (28.6) 428 60 (12.6)STYH BR24 BR24 Binam 450 18 (32.0) 439 97 (11.3)STYH BR24 BR24 OM1723 435 31 (26.2) 413 72 (9.4)STYH BR24 BR24 OM1723 419 17 (22.0) 425 49 (5.4)STYH BR24 BR24 Binam 435 14 (30.6) 382 50 (8.2)STYH BR24 BR24 Binam 241 8 (31.4) 305 40 (7.0)STYH BR24 BR24 Binam 443 21 (23.5) 403 51 (6.7)STYH BR24 BR24 OM1723 120 9 (29.3) 112 20 (10.1)STYH BR24 BR24 OM1723 315 15 (31.0) 220 3 (4.5)Average 358.6 18.1 (27.7) 339.1 47.6 (7.9)
  • Field screening of the 2nd round DQP F2populations under severe lowland stress (2005-2006 dry season) F2 population Male Female IR64 PDL1 PDL2
  • F2 populationParental ILs and IR64
  • Field screening of the 2nd round DQP F2populations under severe upland stress (2005-2006 dry season)
  • Field screening of the 2nd round DQP F2 populations under severe upland stress (05-06 dry season) Controlled irrigated condition Population DK47 DK158 IR64 Lowland stress Population DK47 DK158 IR64
  • Field screening of the 2nd round DQP F2 populations under severe upland stress (05-06 dry season) Controlled irrigated conditionPopulation DK47 DK109 IR64 Lowland stress Population DK47 DK109 IR64
  • Uses of ILs formolecular recurrent selection (MRS)
  • Molecular Recurrent Selection (MARS) Systems for ImprovingMultiple Complex Traits for Different Target Environments Based on Trait-Specific ILs and Dominant CMS (under the way)Composition of the MRS populations: 50+ ILs/PLs carrying favorable QTL alleles from different donors plus the DCMS line in the same genetic backgrounds HHZ MRS population MRS population in a New GB from CMS plants to from CMS plants to Bulk harvest seeds Bulk harvest seeds be screened for be screened for target traits target traits Selected plants enter genotyping and next Selected plants enter the progeny testing, genotyping and next the progeny testing, round of RS round of RS Ovals or boxes of different colors represent different ILs Normal plants carrying genes/QTLs for different target traits CMS plants
  • On-going MRS in phase II of the GSR project Each MRS population consisting of many ILs/PLs of the same elite GB Each MRS population (remove plants with undesirable traits) 50% fertile plants 50% DMS plants ContinuedIrrigated Rainfed Rainfed introgression Flood Biotic breeding/DQP (YP) lowland upland prone stresses New MRS for New Improved next round ILs/PLs lines for PT New lines for PYT Continuation RYT and NCT of MRS under different target Es Genotyping for gene/QTL discovery, confirmation and Farmers in dif. monitoring trait improvement target Es
  • Breeding Procedure of Molecular Recurrent Selection (MRS) improvement based on genetic information Genome selection and trait design and Material platform for Multiple MRSTechnology for pyramiding multiple of the parents of MRS populationsfixation based on combined genome large scale MB populations genes/traits and quick progeny NS Continued and phenotypic selection IB and 50% fertile plants pyramiding 50% MS plants PS Screening Screen Screen for Yield abiotic stress quality biotic stress NS traits tolerances traits resistances Superior ILs/PLs Random mating Cross progeny testing population for PS for multiple traits and next round MRS confirmation NS Preliminary yield trial of promising lines Continued MRS PS = positive selection Multi-location yield trials Genome of promising lines sequence NS = negative 、 SNP genotyping、gene/QTL information selection 、 discovery、allelic mining and platform of Demonstration & confirmation, trait design and the rice core PVS in the target improvement collection environments
  • Conclusions• There are tremendous amounts of hidden genetic diversity for almost all complex phenotypes in the primary gene pool, and selection of parental lines based on phenotype practiced by most breeders is a Development of rice cultivarsn and poor way to exploit this hidden diversity.• discovery of genes/QTLs for complex Backcross breeding, effective selection (screening) combined with DNA markers are the effective way phenotypes can be and should be to discover and exploit this hidden diversity. integrated.• The genetic network for complex phenotypes are very complex - large number of loci and multiple functional alleles at most of the loci.
  • Thank you for your attention!