GRM 2011: Practical application of markers to breed drought-tolerant rice

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GRM 2011: Practical application of markers to breed drought-tolerant rice

  1. 1. Practical application of markers:drought tolerant rice• G4005.69.01 (CB19a/RF−FS022):Developing and disseminating resilientand productive rice varieties fordrought-prone environments inIndia:2005-2009• G3007.05: Detecting and fine-mapping QTLs with major effects onrice yield under drought stress fordeployment via marker-aidedbreeding:2006-2010Arvind KumarInternational Rice Research Institute
  2. 2. Outline• QTLs for grain yield under drought: limitations• MAB of DTY12.1 to improve drought tolerantcultivar Vandana• IR64 lines with four DTY QTL: ABQTL• MAB of DTY1.1, DTY3.1, DTY2.2 QTLs in Swarna sub1• A QTL with consistent effect in multiple highyielding genetic backgrounds• Lessons learnt
  3. 3. • Major drought yield QTLs: true and effective• QTLs x genetic background interaction: a constraint• QTLs identification in improved genetic background- varietythat needs improvement – IR64, Vandana, Swarna, SambhaMahsuri, MTU1010, Sabitri, TDK 1 sub 1, NSICRc 222, BR11,Saro 5• Effect of individual QTLs 300-500 kg ha-1, pyramid two-threeQTLs to get 1.0 t ha-1 or more yield advantageQTLs for grain yield under drought: limitations
  4. 4. Improving drought tolerant cultivarVandana:DTY12.1• DTY12.1 identified inVandana/Way Rarem (Bernieret al. 2007)• Contributed by susceptibleparent- Way Rarem• Mapped to 2.7 Mb (RM28048-RM28166• Consistent effect in targetlocations (Bernier et al. 2009)• Minor QTLs affecting GY andrelated trait contributed bydrought tolerant parentVandana (Bernier et al. 2007)Minor QTLs• DTY2.3 – RM1367-RM3212:(panicle m2)• DTY3.2 –RM7332-RM545:(biomass)
  5. 5. Fine mapping DTY12.1• DTY12.1A- 0.8Mb (RM28099-RM511• DTY12.1B- 0.1 Mb (RM1261-RM28166)• Both regions show effect insevere, moderate, milddrought stress• Effect increases with stressseverity (Bernier et al.2009)• DTY9.1, DTY2.1 and DTY2.2were also fine mappedDixit et al. 2011, TAG under revision
  6. 6. Fine mapping and introgression strategy for DTY12.1
  7. 7. Way Rarem Vandana IR90020:22-283-B-4-BGenotypesUpland severe stress Upland non- stressGY DTF PHT BIO HI GY DTF PHT BIO HIIR 84984-83-15-481-B 693 64 75 4160 0.17 2525 62 79 9584 0.29IR 84984-21-19-78-B 478 66 74 3333 0.13 2996 65 89 10769 0.31IR 90020:22-283-B-1-B 604 66 79 4160 0.14 3039 66 85 11610 0.29IR 90020:22-283-B-4-B 515 67 77 4133 0.21 2245 68 84 7579 0.27Way Rarem 0 NF 60 266.7 0.01 1660 87 100 NA NAVandana 27 70 79 2080 0.09 2127 68 91 10498 0.34Apo 0.1 NF 57 226.7 0 2127 80 101 NA NAApoPerformance of NILs under severe upland stressDixit et al. 2011 Plant Physiology, submittedIRRI, 2011 DS
  8. 8. 05001000150020002500Non- stress Mild stress Moderate stress Severe stressStress connditionPercentageadvantageoverVandanaIR84984-83-15-851-B IR84984-83-15-332-B IR84984-83-15-481-BIR84984-21-19-48-B IR84984-83-15-330-BqDTY12.1 NILs advantage over Vandana undervarying stress conditions: Line source: IRRIDS2011
  9. 9. Way Rarem SwarnaVandana + NIL IR84984-83-15-481-BSeeding date Feb 1Stress initiation Feb 5Harvest date May 15Days with rainfall >5mm during theexperimentMarch 1 -13 60.0 mmApril 29 6.3 mmMay 8 60.0 mmMay 11 38.0 mmTotal 164.3 mmSwarna+NILSwarnaWayRarem Vandana
  10. 10. Grain type of donor parent (Way Rarem), recipient parent (Vandana), NIL (IR90019:17-156-B) and pre NIL(IR90019:17-15-B)Vandana QTL lines are under testing in India (4), Philippines (2)
  11. 11. DTY12.1 interactions with minor QTLsEco-systemqDTY12.1-qDTY2.3Class mean++ +- -+ -- Add.USS-I 913 519 332 202 43.5USS-II 533 428 242 200 16.7UNS-I 3298 2991 3143 2851 5.2UNS-II 3032 2533 2861 2703 9.3Eco-systemqDTY12.1-qDTY2.3Add.Class mean++ +− −+ −−LSS1169 1012 1076 804 8LMS1542 1201 1429 1381 12.1LMiS2618 2566 2544 2498 1.1Upland Lowland
  12. 12. Designation Non-Stress Mild Stress Moderate stress Severe StressIR84996-4-1-B 2457 1859 772 236IR84996-50-1-B 4242 2319 1428 251IR84996-50-4-B 2831 1859 1091 172IR84996-50-6-B 3942 2254 1187 148IR84996-72-6-B 2304 2229 1115 127Way Rarem 2126 1224 601 58Vandana 1976 1535 376 405APO 2445 1882 1199 130Trial mean 2379 1606 890 118p value <0.0001 <0.0001 <0.0001 <0.0001Way Rarem lineswith QTLDTY2.3Dixit et al. 2011, Molecular Breeding, submitted
  13. 13. IR64: DTY2.2, DTY4.1, DTY9.1, DTY10.1 introgression• Aday sel/4*IR64 ABQTL analysis• 6 mapping populations developed(IR77298-14-1-2-10, IR771298-5-6-18) with (IR64, IR77298-14-1-2-13,IR771298-5-6-11)Chr MinOf5p MaxOf3p MinOfFisherP size (BP)2 10,147,149 10,886,276 2.80E-02 739,1274 12,522,585 13,220,820 3.84E-04 698,2356 22,708,740 23,455,589 2.95E-02 746,8499 5,028,455 5,490,310 2.57E-02 461,855Regions identified by Affy-chip analysisHei Leung and Mauleon Ramil, IRRI, unpublished
  14. 14. Population Year Chrom. Marker Interval F R2 AdditiveeffectP1 DS09 9 RM566-RM24350 39.4 9.6 201.7P1 DS10 9 RM566-RM24350 36.7 8.2 89.2P1 (Combined) DS09&DS10 9 RM566-RM24350 50.9 13 134.4P2 DS09 9 RM566-RM24350 77.2 19 352.6P1 DS09 2 RM236-279 28.6 6 166.7P1 DS10 2 RM236-RM279 19.5 9.3 105.5P1 (Combined) DS09&DS10 2 RM236-RM279 37.3 9.1 121.8P4 DS08 2 RM236/RM279-RM555 35 11 112.8P3 DS10 2 RM236-RM279 108.3 3 147.5P3 DS1010RM258-RM25694 28.7 17 298.1P4 WS074RM335-RM518 14.7 11 127.1Major QTLs in IR64 background
  15. 15. Line QTLs DF PH GY GY GS(%)(NS) (NS) (NS) (S)DS11 DS11 DS10 DS11 DS10 DS11IR 87729-69-B-B-B DTY9.1, DTY2.1, DTY10.1,DTY4.183 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 690IR 64 + QTLs lines
  16. 16. IR64 QTLs lines under non-stress andstressIR64+ QTL line Drought Stress2011DS, IRRINon-Stress2011 DS, IRRI+ QTL line IR64IR64 QTL lines under testing in WS2011 at 14 locations in India underAICRIP program; Nepal (03), Bangladesh (01), Philippines (01), and willbe under testing in Tanzania and Mozambique in 2011-2012
  17. 17. Swarna sub 1 + drought• Three drought yield QTLspyramided in Swarna sub1• BC4F2 population with threeQTLs under test at IRRIDTY1.1, DTY3.1, DTY2.1 pyramidedSwarna Swarna + DTY- QTL + QTL - QTLDTY3.1: Hazaribagh, 2008
  18. 18. Dhagaddeshi x Swarna Dhagaddeshi x IR64Dhagaddeshi x Swarna Dhagaddeshi x IR64N22 × Swarna 30.20%N22 × IR64 25.80%N22 × MTU1010 16.90%Dhagaddeshi ×Swarna24.80%Dhagaddeshi ×IR64 8.55%Additive effects in fivepopulations for grain yieldunder droughtDTY1.1: multiple donors - multiple backgroundsVikram et al. 2011, BMC Genetics under revision
  19. 19. Meta analysis of DTY QTLsMQTL AIC value Mean phenotypicvariance of theQTLsMean initial CI(cM)Physical lengthof MQTL(Mb)MQTL1.1 146.2 16 7.5 1.14MQTL2.1 62.7 12 10.5 1.24MQTL3.1 45.2 13 5.4 0.84MQTL10.1 61.8 4 13 5.3MQTL12.1 21.2 28 4.2 0.7Testing the effect of QTLs on a set of drought tolerant panel lines0102030405060708090QTL1.1QTL1.2QTL2.1QTL2.3QTL3.1QTL3.2QTL4.1QTL4.2QTL4.3QTL6.1QTL8.1QTL12.1DTY QTLsDroughtpanellines(%)Swamy et al. 2011, BMC Genomics
  20. 20. Synteny and comparative map of QTLs inrice and maizeDTY1.1 region in rice – Maize 3, wheat 4B, barley 6HDTY3.1 region in rice – Maize 1Swamy et al. 2011, BMC Genomics
  21. 21. Lessons learnt• Combine MAB with accurate drought phenotyping to identifybest lines.• Initially select larger number of fixed lines with QTLs forinsect, disease and quality analysis.• Some of the QTLs regions contain within them loci withnegative effect on GY. Fine mapping and identification of suchalleles necessary .• Some of the DTY QTLs are linked to early flowering and tallheight; larger population in BC1, BC2 to break the linkage,select the desired segregants.• Variety to be improved and donor combination should besuitably decided before initiation of QTL study.• Know the requirements of the national systems.
  22. 22. BANGLADESH NEPAL INDIA AfricaRiceLAOS PHILIPPINESTANZANIA MOZAMBIQUE2008-BMGF – Varietal Improv.2011 - BMGF JAPAN BREEDINGBMZRAJGAZRRSNRRPNDUATUASIGAUCRRITNAUCRURRSBAUBFDASRCIIAMRCCRCPHilRiceReplicated MET undermanaged stress and full irrigationNational testingTargeted Dissemination2007 GCP- QTL identificationOn farmtestingDrought Breeding Network: 2005 GCP-RF: Network testingInitial testing 300-500 lines understress & control – OYT-AYTRDA, KoreaMalaysiaDevgen2011 GCP: Communitypractice, MARS
  23. 23. DonorsGeneration Challenge programRockefeller FoundationBill and Melinda Gates FoundationAsian Development BankDevgenRDA, KoreaBMZ, GermanyUniv. Kebangsaan Malaysia, BangiPartnersBangladeshBRRI, GazipurRRS, RajshahiIndiaAAU, AnandBAU, RanchiBF, HyderabadCRRI, CuttackCRURRS, HazaribagDRR, HyderabadICAR-NEH, TripuraIGAU, RaipurJNKVV, JabalpurNDUAT, FaizabadOUAT, BhubaneshwarTNAU, CoimbatoreUAS, BangaloreNepalNRRP, HardinathRARS, NepalganjRARS, TarharraPhilippines – PhilRiceLaos – NAFRIMozambique-IIAM, ChokweTanzania –DASRC, MorogoroMalaysia – UKM and MARDIRDA, KoreaDevgenThank you very much for your attention

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