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Drought molecular breeding in rice, 19 november, 2012 swamy

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  • 1. Mapping and Transferring QTLs for drought tolerance in rice B.P. Mallikarjuna Swamy November, 19, 2012 Molecular Breeding Course 2012
  • 2. Rice production• Rice cultivated on around 150 m ha• 45% of this area is rainfed• Average rice productivity in rainfed area is less than half of that in irrigated areas• No possibility to expand the irrigation facility due to shrinking water resources• Needed increased rice production to meet the growing demand can only be met through increased productivity in rainfed ecosystem
  • 3. Drought Region Rice area (M ha) Drought-prone rice area (M ha) Upland Rainfed Upland Rainfed Lowland Lowland E. Asia 0.6 2.0 0.6 0.5 S. Asia 7.3 33.2 7.3 8.5 S.E. 2.7 20.8 2.7 4.3 Asia 80% rice area in Sub Saharan Africa is rainfed 57 64 69 73 78 85 90 95 Control Lafitte, unpublishedO’Toole 1982
  • 4. Varieties currently grown in drought prone areas• Most of the high yielding varieties grown in rainfed areas are highly susceptible to abiotic stresses• IR64, MTU 1010, Swarna grown in drought prone area are high yielding but highly susceptible to drought
  • 5. What it takes to develop a drought tolerant variety?• High yield under normal situation• Tolerance to drought at reproductive stage• Tolerance to drought at seedling and vegetative stage• Tolerant to blast, brown spot, bacterial leaf blight• Ability to withstand delayed transplanting conditions• Ability to yield well under low-moderate fertilizer management• Ability to be grown under direct seeded situation in case of unavailability of water for transplanting• Good grain quality/quality maintenance under drought• High framers’ preference• National system support• Efficient dissemination support
  • 6. Drought Research at IRRI: StrategyConventional approaches• Use improved pre-breeding lines as donors• Direct selection for grain yield• Combine high yield potential with good yield under drought• Confirm performance in multi location testing in target environment-Drought breeding networkMolecular approaches• Use traditional/wild donors in mapping populations• Identify major drought yield QTLs• Introgress QTLs in improved drought susceptible varieties• Physiological and molecular mechanism of QTLs drought tolerance
  • 7. Direct selection for grain yield under drought stress Population Situation Heritability rg     S NS   IR 55419-04/Way  Upland  0.45 0.61 0.31 Rarem   Upland  0.66 0.47 0.21 IR 55419-04/IR  Upland  0.49 0.48 0.67 64   Upland  0.52 0.67 0.22 Abhaya/Safri 17 Lowland 0.67 0.41 0.20   Lowland 0.62 0.53 0.36   Lowland 0.59 0.56 0.38   Lowland 0.58 0.68 0.32 6000 Grain yield kgha-1 5000 Selection 4000 Environment Moderate Natural Severe stress stress stressGrain yield (kg ha -1) 3000 2000 Drought stress Non stress 1901 1030 a 581 a 1000 Irrigated control 0 Random 1861 1031 a 561 a Abhaya Safri 17 IR79907-B- IR79913-B- IR64 R2038-2 IR55419-04 Way Rarem Stress 2150 1250 b 791 b 406 176 LSD0 0 . 05 360 111 131
  • 8. Precise drought phenotyping 30-60% reduction- moderate drought 65-85% reduction- severe drought GenotypeFarmer’s field (UP, India; Oct. 2007)Yield & stability, adaptation, quality etc. NARS on-station MET (CRRI Cuttack, India): Yield, GxE, Crop adaptation, acceptability IRRI Field: yield & growth processes, traits IRRI Greenhouse: whole plant responses & processes Environment & Management Platforms e.g. phenopsis INRA-Fr HTP linkage Gene function- plant/cellular processes
  • 9. DS, IRRI vs. WS, NARES screening r=0.57 Reproductive stage drought Irrigated control 60-85% GY reduction - SevereVerulkar et al. FCR 117 30-60% GY reduction - moderateIRRI, DS India, WS
  • 10. Molecular approaches to improve drought tolerance in rice• Identification of major QTLs for grain yield under drought• QTL X environment and QTL X genetic background interaction under drought• Major QTLs in background of mega varieties• QTLs effective against multiple genetic backgrounds• Introgression of major QTLs in popular varieties IR64, Swarna, Swarna sub 1
  • 11. Approach• Large mapping populations (400-500) from crosses of drought tolerant donors with mega varieties• Phenotyping of mapping populations in dry season in managed cyclic severe stress that reduces yield by 65- 85% as compared to irrigated yields• Genotype the population following selective genotyping/BSA approach, add additional markers in the region found to possess QTLs• Validate the effect of QTLs in target environments on a set of lines with and without QTLs• Fine map and introgress the QTL in mega varieties for which identified
  • 12. Molecular Approaches for efficient drought Breeding 1. Identification of QTLs 2. Transfer of QTLs in Mega Varieties Identification of Major QTLs in the background of Mega Varieties-IR64, MTU1010, Swarna, Sambha Mahsuri Mega Varieties ( Swarna,Drought tolerant donor(e.g.N22) X Sambha Mahsuri,MTU1010, QTL Transfer in Mega varieties IR64) Fine Mapping Candidate gene analysis F1 F2 ( take single seed from each Phenotyping in next F2 F2plant) season with F5 plants for Grow single F3 plant validation of QTLs. and harvest individually Identification of large effect QTLs for yield Phenotyping with single plant harvest as F4 progeny. + Genotyping (Parental survey, BSA or Selective genotyping, whole under drought. genome scan with SSR markers)
  • 13. Efficient, cost effective strategy: BSA foridentifying consistent QTLs N22    IR64    BH      BL      N22     IR64     BH       BL QTL identification in multiple  populations simultaneously RM431 Dhagaddeshi Dhagaddeshi Identify few markers in BSA Swarna Swarna BH BH BL BL BSA with adjoining markers  of the identified one RM11943 RM431 Validation of BSA results ADVANTAGES of BSA Consistent Drought Grain Yield QTLs  Cost effective Identified  via BSA Can be applied with expensive marker systems like SNP qDTY1.1; qDTY2.2; qDTY3.1;  (Becker et al. 2011-Plos One) qDTY3.2; qDTY4.1; qDTY6.1; qDTY12.1 RNA can be pooled for microarray (Kadam et al. 2012) Vikram et al. 2012, FCR
  • 14. Why rice is a suitable case for MAB for GY under drought?In rice at IRRI• Many QTLs reported with – Consistent effect in different environments – Consistent effect in different genetic backgrounds – Consistent effect in different ecosystems – Products developed with increased GY
  • 15. Major effect QTLs for grain yield under drought PhenotypicVariety QTL Donor Ecosystem Additive effect variance (R2)Vandana qDTY12.1 Way Rarem Upland 47 33 IR64 qDTY1.1 N22 Lowland 24 17 qDTY2.2 Adaysel Lowland 14 6 qDTY4.1 Adaysel Lowland 6 11 qDTY9.1 Adaysel Lowland 29 19 qDTY10.1 Adaysel Lowland 18 17 Swarna qDTY1.1 N22 Lowland 29 13 qDTY1.1 Dhagaddeshi Lowland 25 32 qDTY2.1 Apo Lowland 23 7 qDTY3.1 Apo Lowland 30 27 Sabitri qDTY12.1 IR74371-46-1-1 Lowland 25 47 qDTY3.2 IR77298-5-6-18 Lowland 16 19SambaMahsuri qDTY11.1 IR55419-04 Lowland 32 14 TDK1 qDTY3.1 IR55419-04 Lowland 10 7 qDTY6.1 IR55419-04 Lowland 12 9 qDTY6.2 IR55419-04 Lowland 16 10
  • 16. How real are DTY? DTY QTLs % of linesTesting QTLs in a panel of DTY1.1 6490 tolerant lines DTY2.1 49 DTY3.1 77Meta-QTL analysis DTY8.1 52 DTY12.1 85 Chr region Mean Initial MQTL MQTL MQTL PV CI (cM) (cM) (Mb) MQTL1.1 1 RG109–RM431 12 7.60 2.40 0.36 MQTL2.1 2 RM452–RM521 12 10.50 5.28 1.24 MQTL2.2 2 RM526–RM497 6 12.00 11.50 2.36 MQTL3.2 3 RM520– M16030 20 10.30 3.40 0.98 MQTL10.2 10 RM596–RM304 16 15.00 23.72 2.60 MQTL12.1 12 RM277–RM260 28 4.20 1.79 0.70 M. Swamy et al. 2011, BMC Genomics
  • 17. Synteny and comparative map of QTLs in rice and maize DTY1.1 region in rice – Maize 3, wheat 4B, barley 6H DTY3.1 region in rice – Maize 1 M. Swamy et al. 2011, BMC Genomics
  • 18. DTY 1.1 :Large effect QTL across thebackgrounds N22/ N22/ IR64 N22/ Swarna MTU1010 Population N22/MTU1010 N22/IR64 N22/Swarna Interval RM315-RM12023 RM11943-RM431 RM11943-RM431 RM315 Chromosome 1 1 1 2.36 Mb Additive Effect (Kg/ha) 375.8 0 335.92 605.24 RM12023 Population mean ( Kg/ha) 2092.15 1645.05 1589.9 Additive Effect % of Trial mean 17.96 % 20.42% 38.06% F-value 37.59 41.47 68.76 Chromosome1 Prashanth et al. 2011, BMC Genetics
  • 19. qDTY 1.1 effect across ecosystem, environments & backgrounds AdditivePopulation Ecosystem Location Reference effect*CT9993-5-10-1- Raipur, 20.6 Lowland Kumar et al. 2007M/IR62266-42-6-2 IndiaApo/IR64 52.2 Upland IRRI Venuprasad et al. 2011Apo/IR72 63.6 Upland IRRI Venuprasad et al. 2011IR64*2/Azucena 36.2 Upland IRRI Venuprasad et al. 2011Vandana/IR64 25.6 Upland IRRI Venuprasad et al. 2011Vandana/IR72 63.4 Upland IRRI Venuprasad et al. 2011N22/IR64 24.3 Lowland IRRI Vikram et al. 2011N22/MTU1010 16.1 Lowland IRRI Vikram et al. 2011Dhagaddeshi/Swarna 24.9 Lowland IRRI Ghimire et al. 2012Dhagaddeshi/IR64 8.3 Lowland IRRI Ghimire et al. 2012 * Maximum additive effect as the % of trial mean Prashant, IRRI
  • 20. qDTY3.1 : Major effect and consistent QTL in Swarna and BR11 Additive Recipien QTLs Chr Interval R2 Donor effect t DTY3.1 RM520- 3 30 25 Apo Swarna RM16030 DTY3.1 RM15935- 3 20-25 22 Apo BR11 RM520 Apo x Swarna Apo x BR11 Swamy, IRRI
  • 21. First major QTL for grain yield under drought in rice -DTY12.1 CHR. 12 FINE MAPPED REGIONRM247 3.1 Mbp DTY12.1RM3472 3.8 Mbp 14.1 RM 28048 16.1 Ind 8RM3103 7.4 Mbp 15.1 RM 28076RM7195 9.8 Mbp 15.4 RM 28089RM28048 14.1 Mbp 3.5 Mbp 15.8 RM 28099 16.7 RM 28130RM511 17.3 Mbp 0.6 MbpRM1261 17.5 Mbp 16.1 Ind 8 16.5 Ind 4 17.3 RM 511RM28166 17.6 Mbp 16.7 RM 28130 0.3 MbpRM3739 24.9 Mbp 17.3 RM 511 17.6 RM 28166RM235 26.1 Mbp 17.5 RM 1261RM17 26.9 Mbp 17.6 RM 28166 Identification Fine mapping on For further confirmation BC2 in BC2 and BC3 21 populations
  • 22. DTY12.1 grain yield under two water regimes Mild stress Severe stress
  • 23. Large effect drought QTLs• qDTY 1.1 , qDTY 2.3 , qDTY 3.1 , qDTY 3.2 , qDTY 12.1 shows effect against- – Different drought susceptible recipient varieties – Different environments – Across both lowland and upland ecosystem • No guarantee if MAB is not carried by an experienced drought breeder as many minor modifications are needed during the process of MAB
  • 24. Major drought yield QTLs in background of improved popular varieties: IR64 Genetic Additive effect asBackgrounds QTLs Ecosystem % of trial mean IR64 DTY9.1 Lowland 27 IR64 DTY10.1 Lowland 22 IR64 DTY2.1 Lowland 13 IR64 DTY4.1 Lowland 14 IR64 DTY1.1 Lowland 32
  • 25. QTLs in IR64 Back ground P4, 2007WS P1, 2009DS P1, 2010DS P3, 2010DS P4, 2008DSDTY2.2 DTY4.1
  • 26. IR 64 introgression lines with DTY QTLs: AB QTL approach + QTL - QTL IR64 IR64+DTY QTLs Introgressions under drought- 2010 Parents- 2007 DTY IR 64 introgressed lineSimilar to IR64 grain quality traits of Product - 2011introgressed lines
  • 27. IR64 QTLs lines under non-stress and stress + QTL line Non-Stress IR64 + QTL line Drought Stress IR64 2011 DS, IRRI 2011DS, IRRIIR64 QTL lines under testing in WS2011, WS2012 at 14 locations in Indiaunder AICRIP program; Nepal (03), Bangladesh (01), Philippines (01),
  • 28. IR64 QTLs lines under non-stress and stressLine QTLs DF(NS) PH(NS) GY(NS) GY(S) GS (%) DS11 DS11 DS10 DS11 DS10 DS11IR 87729-69-B-B-B DTY9.1, DTY2.1, DTY10.1, DTY4.1 83 91 4312 6308 2011 1943 94.4IR 87728-491-B-B DTY9.1, DTY2.1, DTY4.1 82 95 - 6232 1041 1879 92.6IR 87707-186-B-B-B DTY2.1, DTY10.1, DTY4.1 78 99 4550 6103 2068 2632 96.9IR 87707-446-B-B-B DTY2.1, DTY4.1 80 98 3752 4388 2556 3000 97.0IR 87707-445-B-B-B DTY2.1, DTY4.1 77 96 5045 5844 2555 3023 96.9IR 87728-162-B-B DTY9.1, DTY2.1 84 94 - 6115 1147 1636 92.4IR 87705-83-12-B DTY2.1, DTY10.1 80 95 4796 5526 1916 2270 95.0IR 87705-80-15-B DTY10.1, DTY4.1 81 89 3850 5516 2074 2151 94.6IR64 80 96 2987 5435 636 1442LSD0.05 3 7 1053 690 IR64 IR64 IR64 + QTL line + QTL line IR 87707-445-B IR 87707-182-B IR64 Drought Stress2011DS, IRRI CRURRS, Hazaribag, India 2011 WS PLOS One ( In review )
  • 29. Quality traits of IR64 introgression linesLINES QTLs DTF PH AC GT MP CSIR 87729-69-B-B-B DTY9.1, DTY2.1, DTY10.1, DTY4.1 86 98 20.7 I 1 1IR 87728-102-B-B DTY9.1, DTY10.1,DTY4.1 86 101 20.1 I 1 1IR 87707-186-B-B-B DTY2.1, DTY10.1,DTY4.1 82 107 21.6 I 2 1IR 87707-446-B-B-B DTY2.1, DTY4.1 81 106 22.2 I 1 1IR 87707-445-B-B-B DTY2.1, DTY4.1 83 111 22.3 I 1 1IR 87707-118-B-B-B DTY2.1, DTY4.1 83 108 20.7 I 1 1IR 87705-21-13-B DTY2.1 82 86 21 I 2 1IR 87705-6-8-B DTY4.1 80 85 21 I/L 2 1IR 87728-395-B-B DTY9.1 86 100 20.2 I 1 2IR 87705-36-3-B DTY10.1 87 84 20.3 I 1 1IR64 82 105 21.8 I/L 1 1 M. Swamy, IRRI
  • 30. IR64 drought tolerant NILs under upland drought GY GY DTF DTF HT HT Kg/ha Kg/haENT DESIGNATION NS S NS S NS S 1 IR 87707-446-B-B-B 77 89 72 69 2844 576 2 IR 87707-445-B-B-B 75 90 IR64 77 64 2800 471 IR64+DTY QTLs 3 IR 87707-182-B-B-B 78 89 69 59 2863 451 4 IR 87707-118-B-B-B 83 93 82 74 1209 102 5 IR 87729-69-B-B-B 80 95 80 56 2073 97 6 IR 87706-215-B-B-B 80 90 61 51 1506 174 7 IR 87705-44-4-B-B 78 95 81 50 1861 113 8 IR 87705-14-11-B-B 78 90 61 61 2180 439 9 IR 87705-83-12-B-B 83 95 69 54 1920 11410 IR 87728-102-B-B-B 86 95 76 54 1383 64 96 IR11 IR64 83 90 77 65 1542 54 * 500 Kg yield advantage over IR64 under upland drought
  • 31. Improved drought tolerant IR64 lines under lowland drought in target environments Grain yield (kg ha-1) Rajshahi Nepalganj Raipur Hyderabad 1 Hyderabad 2 Hazaribagh RewaEntry NS DS NS DS NS DS NS DS NS DS NS DS NS DSIR87707-445-B-B 4167 1525 5990 3472 5084 3956 5672 1684 5672 3800 5690 1604 4100 3731IR87707-446-B-B 4521 1933 6302 2847 5771 3614 5634 1813 5634 4057 5711 1229 4911 3899IR87707-182-B-B 4312 1508 6510 2778 5646 3419 6047 1383 6047 3604 4453 1500 4513 3509IR64 3379 980 4297 1597 4083 2662 5699 660 5699 3085 5612 958 3586 2503LSD 240 156 324 170 434 285 186 939 186 600 475 422 920 909 * 500 to 1500 Kg yield advantage over IR64 under lowland drought Swamy, 2012
  • 32. Introgression of major effect drought grain yield QTLs DTY3.1 and DTY12.1 Anjali IR81896-B-195 X Anjali (DS2010) Fore ground selection Major effect drought grain yield QTLs ( DTY3.1) Additive QTLs Chr Interval R2 Donor F1 X Anjali (WS2010) Fore ground selection effect DTY3.1 3 RM520-RM16030 30 25 Apo BC1 X Sub1Swarna (DS2011) Fore ground selection DTY 12.1 12 RM28048- 36 47 Way Rarem RM28166 Fore ground selection BC2F1 (WS2011) Selection of BC2F2 (DS2012) homozygote for DTY3.1 IR 84984-83-15-18-B-B-93 X Anjali (DS2010) Fore ground selection ( DTY12.1) F1 X Anjali (WS2010) Fore ground selection BC1 X Sub1Swarna (DS2011) Fore ground selection Anjali lLs with DTY12.1 , 12DAS Fore ground selection BC2F1 (DTY3.1) X BC2F1 (DTY12.1) (WS2011)Fore ground selection Selection of homozygote for DTY12.1 BC3F1 BC2F2 (DS2012) Selection of homozygote for DTY3.1 and DTY12.1 Selected homozygotes with DTY3.1, DTY12.1 and their Anjali lLs with DTY3.1 12DAS BC3F2 (WS2012) combinations will be tested under drought DS2013 Swamy, IRRI
  • 33. Improving Swarna and SwarnaSub for drought tolerance• Pyramid four drought yield QTLs- DTY 1.1 , DTY 3.1 , DTY 2.1 and DTY 8.1 to improve yield of Swarna Swarna by 1.2-1.5 t/ha• Pyramid three drought yield QTLs – DTY 1.1 , DTY 3.1 , DTY 2.1 to improve yield of Swarna sub1 by 1.0-1.2 t/ha Swarna sub1+ DTY QTLs
  • 34. Pyramiding of major effect drought grain yield QTLs DTY1.1, DTY2.1 and DTY3.1 in Swarna Sub1:MAB Pyramiding two QTLs Major effect drought grain yield QTLs in Swarna Fore ground selection AdditiveIR81896-B-195 X Swarna(WS2009) QTLs Chr Interval R2 Donor Background selection effect(DTY2.1and DTY3.1) DTY1.1 RM11943- 1 14 30 N22 RM12091 Fore ground selection BC2 X Sub1Swarna(DS2010) Background selection DTY2.1 2 RM327-RM262 16 12.5 Apo DTY3.1 3 RM520-RM16030 30 25 Apo Fore ground selection BC3 X Sub1Swarna (WS2010) Background selection Fore ground selection BC4F1 (DS2011) Background selection Select homozygotes BC4F2 (WS2011) Background selection Drought screening Pyramiding3 three QTLs BC4F (DS2012) BC3 (DTY2.1 and DTY3.1) X BC3(DTY1.1) (WS2010) BC4F1(DS2011) Fore ground selection Swarna sub1 Swarna sub 1 Swarna sub1 lLs with DTY lLs with DTY Select homozygotes QTLs QTLs BC4F2 (WS2011) Drought screening Swamy, IRRI, 2012
  • 35. Pyramiding of major effect drought grain yield QTLs DTY1.1, DTY2.1 and DTY3.1 in SwarnaSub1 Background recovery of Swarna ILsBC4F3 Swarna lLs (Two QTLs + Sub1) Submergence screening 1 day after draining BC4F3 Swarna lLs (Three QTLs + Sub1) 6 days after draining Swarna
  • 36. Performance of Swarna Sub1 three QTL lines: MAB Designation DTF HT GY S QTLs ART5IR96321-558-206 4919 DTY1.1 DTY3.1 DTY2.1 s1IR96321-1080-91 90 103 4479 DTY1.1 DTY3.1 DTY2.1 sIR96321-327-107 4202 DTY1.1 DTY3.1 DTY2.1 hIR96321-327-210 90 93 4022 DTY1.1 DTY3.1 DTY2.1 sIR96321-1099-154 3948 DTY1.1 DTY3.1 DTY2.1 hIR96321-1080-278 86 121 3939 DTY1.1 DTY3.1 DTY2.1 sIR96321-967-412 86 139 3918 DTY1.1 DTY3.1 DTY2.1 hIR96321-967-105 82 136 3909 DTY1.1 DTY3.1 DTY2.1 s1IR96321-1099-44 90 94 3891 DTY1.1 DTY3.1 DTY2.1 s1IR96321-967-57 82 138 3885 DTY1.1 DTY3.1 DTY2.1 sIR96321-558-209 3876 DTY1.1 DTY3.1 DTY2.1 s1IR96321-1393-58 90 89 3855 DTY1.1 DTY3.1 DTY2.1 sIR96321-678-240 89 90 3845 DTY1.1 DTY3.1 DTY2.1 sIR96321-315-374 3836 DTY1.1 DTY3.1 DTY2.1 s1Apo 76 115 2078
  • 37. Effect of DTY12.1 at pre flowering and reproductive stage under severe upland stressand grain types of improved Vandana NILs Vegetative stage Reproductive stage -DTY12.1 +DTY12.1 -DTY12.1 +DTY12.1
  • 38. Development of improved Vandana with DTY12.1 Grain yield (Kgha-1) % Lines Generation DTF PHT USS UMS UNS BGA IR 84984-83-15-110-B BC2F2:4 299 1514 4855 54 124 92.4 IR 84984-83-15-481-B BC2F2:4 175 1300 4196 55 120 94.1 IR 84984-83-15-862-B BC2F2:4 238 1114 4018 58 121 94.1 Vandana 72 825 3556 54 120 Way Rarem 11 212 1610 81 122B IR 90019:17-156-B BC3F2:3 522 1487 4712 61 106 98.3 IR 90019:17-159-B BC3F2:3 461 1930 5236 62 103 97.5 IR 90019:17-15-B BC3F2:3 565 2341 4534 65 107 98.3 IR 90020:22-265-B BC3F2:3 446 2090 4233 60 115 96.6 IR 90020:22-283-B BC3F2:3 415 1224 5950 58 100 94.9 Vandana 179 1049 4061 56 104 Way Rarem 0.1 500 2878 81 103 Dixit, Shalabh, IRRI
  • 39. Performance of Vandana NILs at IRRI and in India Upland severe stress Upland non- stress Designation GY DTF PHT BIO HI GY DTF PHT IR84984-83-15-481-B 693 64 75 4160 0.17 2525 62 79 IR90020:22-283-B-1-B 604 66 79 4160 0.14 3039 66 85 IR90020:22-283-B-4-B 515 67 77 4133 0.21 2245 68 84 Way Rarem 0 NF 60 2667 0.01 1660 87 100 Vandana 27 70 79 2080 0.09 2127 68 91 Apo 0.1 NF 57 2267 0 2127 80 101 PHT Designation DTF GY- C GY-D DTF GY-D IR84984-83-15-481-B 78 116 5670 2343 61 1687 IR90019:22-283-B 78 107 5208 2410 60 1580 VANDANA 81 105 4348 1799 60 1327 WAY RAREM 90 115 4649 868 90 100 IR84894-83-15-481-B Vandana S. Dixit, IRRI; NP Mandal, CRURRS
  • 40. Genomic regions for MARS in IR55419-04 x Samba MahsuriMarker Aided Introgression Additive Chr Interval Trait Effect Donor 1 RM212-RM486 700 Yield -NS IR55419-04 DTY11.1 11 Kid2746 – Kid 287 117 Yield -S IR55419-04 Kid3806 –RM520 Yield -S IR55419-043 and 6 350 Kid1613-Kid3434 1 RM212- RM486 10 Height -NS IR55419-04 2 RM525-RM221 -3 Height -NS IR55419-04 3 RM16-RM520 - Blast IR55419-04Marker Aided Exclusion Additive Chr Interval Trait Effect Donor Kid8590 – Kid 9045 5&6 10 Height- NS IR55419-04 Kid8590 – Kid 9045 Line *RM212 *RM486 *RM525 *RM221 *RM16 *K_id3 *K_id3 *K_id3 *RM520 *K_id6 *K_6 10 IR55419-04 x Samba Mahsuri (MARS) 3 RM175- Kid6808 -149 Yield-S IR55419-04 1 1 2 2 2 1 1 1 1 1 1 30 1 1 3 3 1 1 1 1 2 3 . 31 1 3 1 1 1 1 1 1 2 1 1 80 2 2 2 2 2 1 3 3 3 1 1 82 2 3 3 2 2 1 1 1 1 1 1 84 1 2 1 2 2 1 1 1 1 1 1 FRS 102 109 1 1 1 1 3 2 3 2 1 2 3 1 1 1 1 3 2 3 2 1 1 1 SRS 123 3 3 1 1 1 3 3 1 2 2 1 199 1 3 1 1 1 2 2 3 3 . 3 201 1 1 1 1 1 . 2 1 2 . 1 Interactions for plant height under non-stress
  • 41. Intogression of DTY QTLs in Korean parents (RDA) Back ground Stage QTLs Hanareumbyeo BC1 DTY1.1 and DTY2.2 Jinmybyeo BC1 DTY1.1 and DTY2.2 Gayabyeo BC1 DTY1.1 and DTY2.2 Sagnambatbyeo BC1 DTY1.1 and DTY3.1BC2 – confirmed for foreground markers and will be backcrossed Introgression of QTLs in Smbha Mahsuri• QTLs – DTY2.2 and DTY4.1• Generation - BC2F2• Foreground selection and selection of homozygotes• Background selection
  • 42. MAB to improve MRQ74, MR219 MRQ74 MRQ74 MRQ74 X X X IR84984-83-15-18-B IR81896-B-B-195 IR77298-14-1-2-10 (qDTY12.1) (qDTY3.1) (qDTY2.2) Foreground genotyping for qDTY12.1 Foreground genotyping for qDTY2.2 F1 (145) X F1 (142) Foreground genotyping for qDTY2.2 & qDTY12.1 Foreground genotyping for qDTY3.1 388 (Total) 18 (foreground F1 (18) X F1 (53)genotyping) Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, 743 (Total) 21(foreground genotyping) 10 (PH, background genotyping) F1 (10) X MRQ74 Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, Recombinant & Full background genotyping 878 (Total) 35 (foreground genotyping) 10 (PH, background genotyping) BC1F1 (10) Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, X Recombinant & Full background genotyping BC1F2 (5000) Wet Season 2012 Foreground genotyping for qDTY2.2, qDTY 3.1 & qDTY12.1, (homozygous condition), X Recombinant & Full background genotyping, Selecting lines with different +qDTY combinations and -qDTY Forward breeding BC1F3 Currently at this stage Field Screening (Dry season 2013) Nora, and Swamy IRRI- UKM, Malaysia
  • 43. Pyramiding qDTY3.2 and qDTY12.1 in Sabitri IR74371-46-1-1 X Sabitri IR77298-5-6-18 X Sabitri qDTY3.2 mapped qDTY12.1 mapped BC1F5 [5] X BC1F5 [5] and effect tested and effect tested Plants segregating for qDTY12.1 and Plants segregating for qDTY12.1 and qDTY3.2 identified, background genotyped F1 [300] X Sabitri qDTY3.2 with clearest background to be identified and back crossed to Sabitri Plants segregating for qDTY12.1 and qDTY3.2 with clearest BC1F1 [1000] background identified and selfedPlants with qDTY12.1 and qDTY3.2with clearest background to be F2 [1000] Plants with qDTY12.1 and qDTY3.2identified and seeds multiplied BC1F2 [1000] with clearest background to be identified F3 [1000] BC1F3 Seed multiplication and drought screening Seed multiplication and drought screening Shalabh and Prashant, IRRI
  • 44. Fine mapping DTY2.1, DTY2.2, DTY9.1 and DTY12.1 Original QTL Fine mapped region(s) Length LengthQTL Flanking markers (Mb) QTL Flanking marker (Mb)DTY2.1 RM521-RM262 10.8 DTY2.1 A SS RM521-RM3549 0.3 DTY2.1 B MS RM3549-RM6374 4.5DTY2.2 OSR17-RM12868 7.9 DTY2.2 SS RM279-RM492 4.9DTY9.1 RM464-RM24421 8.2 DTY9.1A MS RM321-RM24325 2.6 DTY9.1B SS RM24350-RM24390 0.9DTY12.1 RM28048-RM28166 2.7 DTY12.1AMiS RM28099-RM511 0.8 DTY12.1B SS RM28130-RM1261 0.5 DTY12.1C MS RM1261-RM28166 0.1 Shalabh Dixit, IRRI
  • 45. IR84984-21-19-62-B-B 2010WS ROS Expt 2b QTL 12.1 IR84984-83-15-481-B-B Vandana Physiology DTY12.1 38 Way Rarem 37 36 -QTL Canopy temp (C)Bernier et al. (2009) : 7% greater 35 34water uptake in +QTL lines under 33drought in lysimeters +QTL 32 31No difference in root depth 30 28 31 36 42 56 70 days after sow ing +QTL lines had lower canopy temperatures during drought stress in the field +QTL lines had greater root branching (larger proportion of fine (lateral) roots) than -QTL lines under drought 83-15-481-B-B (+QTL) 21-19-60-B-B (-QTL)Hypothesis: greater root branching induced by drought stress in +QTL linesimproves water uptake from drying soil Amelia Henry, IRRI
  • 46. Physiology Aday Sel x IR64 NILs -QTL +QTL -QTL IR64 14-1-2-13 5-6-18 5-6-11 In severe drought, +QTL lines showed lower canopy temperature and greater stomatal conductance.• No differences in root length or depth were detected +QTL Aday Sel 14-1-2-10 +QTL lines showed lower root hydraulic conductance, and also smaller root and xylem vessel diameter 14-1-2-10 (+ QTL) 14-1-2-13 (- QTL)Hypothesis: smaller xylem vessels in +QTL lines result in reduced xylem vesselcavitation under severe stress Amelia Henry, IRRI
  • 47. Wild species derived mapping population development SL No Female Parentage Male Parent Rice varietiesDiversity 1 MTU 1010/IRGC 81994 MTU1010based on SSR 2 MTU 1010/IRGC 105757 MTU1010 markers 3 MTU 1010/IRGC 106109 MTU1010 4 MTU 1010/IRGC 106283 MTU1010 5 MTU 1010/IRGC 106285 MTU1010 6 Saro 5/IRGC 81994 Saro 5 7 Saro 5/IRGC 105757 Saro 5 Wild accessions 8 Saro 5/IRGC 106109 Saro 5 9 Saro 5/IRGC 106283 Saro 5 10 Saro 5/IRGC 106285 Saro 5 11 NericaL-14/IRGC 105757 NericaL-14 12 Nerica-L-14/IRGC 106277 NericaL-14 13 Nerica-L-14/IRGC 106285 NericaL-14 14 Nerica-L-31/IRGC 104639 Nerica-L-31 15 Nerica-L-31/IRGC 106277 Nerica-L-31 16 Nerica-L-5/IRGC 106109 Nerica-L-5 17 Nerica-L-7/IRGC 106283 Nerica-L-7 18 Nerica-L-8/IRGC 106285 Nerica-L-8
  • 48. qDTY3.1 : Major effect and consistent QTL in Swarna and BR11 Additive Recipien QTLs Chr Interval R2 effect Donor t • QTL validation DTY3.1 RM520- 3 30 25 Apo Swarna RM16030 • Fine mapping DTY3.1 RM15935- 3 20-25 22 Apo BR11 RM520 • Physiogical characterization • Insilico candidate Apo x Swarna Apo x BR11 gene identification •Transciptome analysis to identify differentially expressed genes • Validation of genes by RT and QRT PCR
  • 49. Conclusions• Major drought yield QTLs are true and effective• Effect of individual QTLs 300-500 kg ha -1 , requires pyramiding of three QTLs to get 1.2 ton or more yield advantage• Major QTLs with effect in the multiple improved genetic background exist• Vandna, Way Rarem, IR64 improved for yield under drought• DTY QTLs introgression in Swarna, Swarna sub 1 have been successfully tested• Introgression, molecular and physiological
  • 50. PartnersBangladesh Philippines – PhilRiceBRRI, Gazipur Laos – NAFRIRRS, Rajshahi Mozambique-IIAM, Chokwe Tanzania –DASRC, MorogoroIndia Malaysia – UKM and MARDIAAU, Anand RDA, KoreaBAU, RanchiBF, HyderabadCRRI, CuttackCRURRS, HazaribagDRR, HyderabadICAR-NEH, Tripura DonorsIGAU, Raipur Rockefeller FoundationJNKVV, Jabalpur Bill and Melinda Gates FoundationNDUAT, FaizabadOUAT, Bhubaneshwar Generation Challenge programTNAU, Coimbatore Asian Development BankUAS, Bangalore DevgenNepal RDA, Korea BMZ, GermanyNRRP, HardinathRARS, Nepalganj Univ. Kebangsaan Malaysia, BangiRARS, Tarharra MARDI, Malaysia