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TLI 2012: Bean research progress report

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  • 1. TL1 meetingProgress in Objective 3: Common beans Bodo Raatz, CIAT Addis Ababa, May 2012 1
  • 2. Road map• Ethiopian program• SNPs – QTLs in the making in MAGIC, MARS, association mapping• Markers in application MAS• Phenotyping 2
  • 3. Mesoamerican Andean Gene Pool Gene PoolCultivated commonbean:• Two major genepools• Specific grainclasses…that define thestructure of breedingprograms 3
  • 4. Activity 2: SNP assay• Collaboration with USDA-Beltsville, mediated by Xavier• 1500 SNPs converted to Kaspar (Kbio)• SNPs chosen that are polymorphic within gene pools and grain classes• 94 lines genotyped (Milestone 2) 4
  • 5. Activity 2: SNP assayPhylogeny analysis … genotypes markers Mesoamerican Andean Phaseolus coccineus Phaseolus acutifolius 5
  • 6. Activity 5.1: MARS PhD thesis of Fitsum Alemayehu SARI, EthiopiaSister lines SABs 626, CAL 143 628, 659, 686 – Released in 6 – Drought X countries in southern Africa – Improved remobilization? – Vegetative vigor – Tolerant of poor soils • 165 markers selected for genotyping • Results in analysis 6
  • 7. Activity 5.1: MARS genotyping 1 2 3 4 BARC-PV-0000055 sc01018ln115966_70654_C_T_3130 sc01018ln115966_84234_C_T_3130 1.4 sc00244ln360837_151643_G_T_157 1.2 sc00518ln214431_82881_A_G_2346 sc00244ln360837_80567_T_C_1578 2.1 sc00518ln214431_38754_C_T_2345 0.4 sc00334ln300981_254308_G_A_187 sc00831ln140879_35627_G_A_2890 sc00377ln276023_97213_T_G_2002 1.0 sc00112ln569344_270381_C_T_979 1.0 0.3 sc00112ln569344_446130_C_T_981 0.7 sc00334ln300981_202658_C_T_187 0.4 sc00112ln569344_538657_G_A_98210.1 sc00964ln122791_59538_A_C_3065 0.4 sc00835ln140787_95095_C_T_2896 sc00429ln249479_88921_A_G_2138 0.7 sc01131ln102720_84539_A_G_3253 0.2 sc00283ln338214_136440_C_T_171 1.9 0.6 sc00283ln338214_153572_G_T_171 10.1 sc00283ln338214_233599_A_C_171 62.3 0.3 sc00283ln338214_239137_G_A_17141.8 66.8 0.8 sc00283ln338214_293493_T_C_171 sc01149ln100495_6599_A_G_32715 sc01149ln100495_19761_C_T_3271 sc01149ln100495_32702_T_C_3271 56.9 sc00043ln806145_763080_A_G_521 sc00477ln232797_55899_C_T_2254 sc00043ln806145_731182_A_G_521 sc00043ln806145_170363_C_A_51614.5 sc00426ln251751_240727_C_T_213 sc00043ln806145_102278_G_A_515 sc00043ln806145_27550_A_G_5145 sc00050ln749641_133318_T_C_569 BARC-PV-0005808 17.5 13.9 sc02743ln31009_27860_A_G_41677 sc00079ln659676_266197_T_C_776 0.8 sc00721ln160814_116732_A_G_27218.6 3.4 sc00458ln240490_238835_A_C_221 3.4 sc00880ln134596_94488_T_C_2958 sc00736ln157270_32680_T_C_2748 2.1 2.0 sc00022ln1003704_490507_A_C_32 sc00134ln519503_497021_C_T_110 1.6 sc00036ln871953_816000_T_G_463 4.0 sc00023ln985577_737723_A_G_342 sc00036ln871953_623598_A_C_461 5.9 2.2 2.5 sc00022ln1003704_88768_G_A_325 sc00023ln985577_404408_A_G_339 3.9 sc00036ln871953_260922_C_A_457 12.7 sc00716ln161188_139140_T_G_27115.3 sc00003ln2130026_318965_G_A_46 17.9 sc00061ln715360_52902_C_T_6499 0.4 sc00003ln2130026_249989_T_G_45 sc00018ln1167623_926274_C_T_29 1.1 sc00003ln2130026_221589_T_C_45 55.1 3.5 sc00018ln1167623_515133_C_A_28 4.0 sc00618ln186586_8943_T_C_25469 6.7 0.2 24.0 sc00018ln1167623_30331_G_T_281 sc01409ln79819_3642_A_C_350551 1.3 sc01035ln113702_42942_G_A_3149 sc01409ln79819_56167_T_C_35060 2.6 0.4 sc00175ln461633_78259_G_T_1298 sc00009ln1640450_1304280_C_T_1 3.9 sc00175ln461633_42284_G_A_1298 sc00914ln129176_38656_G_A_3003 sc00025ln963649_165119_T_G_356 0.7 sc00025ln963649_327459_T_C_357 11.6 sc00038ln842375_5033_G_A_47257 4.1 sc00038ln842375_820428_T_C_480 11.2 sc00027ln946161_647185_A_G_380 0.5 sc00027ln946161_730836_A_C_381 7
  • 8. Activity 5.1: MARS genotyping 5 6 7 8 sc00516ln215718_103432_C_T_234 sc01815ln56854_15487_C_T_37774 sc00431ln249067_99164_A_G_2143 sc00089ln640327_255418_C_T_841 9.7 sc00014ln1397360_934650_A_G_23 3.9 sc00502ln219883_127438_T_C_231 30.7 5.4 sc00067ln694271_486308_T_C_69643.3 8.8 sc00052ln745181_210054_A_G_585 sc00162ln482802_338752_C_T_123 sc00052ln745181_283027_C_T_586 sc00162ln482802_86819_T_G_1236 6.1 sc00064ln701495_548353_A_G_676 1.7 67.2 sc00583ln198651_1233_G_A_24795 9.8 sc00169ln473620_158171_C_T_127 sc00153ln494563_454394_G_A_119 2.7 sc00158ln489092_253333_G_A_121 sc00004ln1947458_369015_C_T_6832.4 sc00004ln1947458_475808_A_G_69 sc00004ln1947458_609051_G_A_70 30.9 sc00004ln1947458_651581_A_G_71 sc01794ln57480_20276_G_A_37654 1.9 sc00004ln1947458_666119_G_A_71 0.3 sc00004ln1947458_704961_G_A_71 1.7 sc00004ln1947458_901631_G_A_73 sc00262ln351368_101277_A_G_164 7.7 sc00004ln1947458_1019379_A_G_7 0.6 sc00004ln1947458_1047835_C_A_7 0.3 0.4 sc00004ln1947458_1101740_A_C_7 4.7 sc00004ln1947458_968323_T_C_74 59.6 sc00004ln1947458_1211738_C_T_7 sc00004ln1947458_1308111_T_C_7 50.4 sc00004ln1947458_1320715_T_C_7 sc00004ln1947458_1733897_T_C_8 BARC-PV-0001413 sc00035ln877458_767887_C_T_454 1.5 sc00002ln2152649_1120369_C_T_3 0.9 11.3 2.1 BARC-PV-0001385 sc00002ln2152649_1550949_T_G_3 sc00187ln435150_76559_G_A_1352 8
  • 9. QTL / association mapping for drought toleranceAndean genepool Mesoamerican genepoolCAL143 NATAL PAN127 R.C. SUG131 SEC16 SEQ11 SER8 SER16 SER22 SUGAR WONDER F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1F1 F1 F1 F1 F1F1 F1 F2 F2 F2 160 plants harvested F3 F3 F4 F4 400 lines F4:6 F4:6 QTL/Association analysis 9
  • 10. SNP set: Regenotyping for improved QTL mapBAT 881 x G21212 330 polymorphic SNPsSER16 X (SER16 X G35346) G35346 = Phaseolus coccineus 400 polymorphic SNPsPinto Saltillo X Pinto Villa 170 polymorphic SNPs 10
  • 11. DNA extraction from seeds Cut seeds DNA extractionAmplification Test seeds macerated with BM 185 stainless steel beads Tissue Lyser 11
  • 12. Cut seeds germinate in the field Seed storage to planting Germination test In field 12
  • 13. Activity 5.2: Advanced backcross• Five Adv. BC populations BC2-F4 SOURCE SER 16 SER 48 CAL 143 126 78 CAL 96 156 128 CIM 9314-36 39 -• Most lines badly adapted• 2012: - few lines in breeding program - QTL appropach abandoned 13
  • 14. Activity 5.2: Advanced backcrossAndean recurrent parent CAL 96 Mesoamerican donor SER 16 14
  • 15. Activity 5.2: Advanced backcross 15
  • 16. MAGIC population in common bean (mesoamerican gene pool)SXB 412 INB 827 ALB 213 SEN 56 SCR 2 MIB 778 SCR 9 INB 841 79 F1 5 F1 38 F1 99 F1 323 F1 272 F1 728 F1 500 selected 499 F2 996 F3 families 996 F3.5 families F5:7 families for drought phenotyping Genotype individuals 16
  • 17. Activity 3: MAS for biotic traitsStorage insects:Bruchids (Zabrotessubfasciatus) 17
  • 18. SSR marker for bruchid resistance PV-ATCT001 – Arc•20 crossesAgarose based marker: SEQ1006 SEQ1027 RAZ105 RAZ106 CAL143 G18264 Blanco RAZ44 Cortesia: H.F. Buendia 18
  • 19. RI = log{(Emerged adults/hatched eggs) + 1} / DAE * 100 Activity 3: MAS for bruchid resistance 3.50 84 3.00 2.50 117 KATB9 125 24 123 63 124 65 67 CAL143 71 25 60 79 82 86 57 58 55 44 80 119 59 70 83 61 75 126 62 76 129 68 72 121 64 122 77 S 81 128 74 127 2.00 66 1 73 12 102 78 40 53 PV-ATCT001 marker 49 112 28 93 99 45 1.50 15 50 16 4 positive 120 41 90 96 95 52 heterozygote 20 111 104 37 54 46 39 100 27 RI negative 1.00 10 36 43 115 6 97 No Amplification 47 29 30 31 94 8 33 17 0.50 13 RAZ103 113 98 87 35 R 23 19 88 105 38 11 21 34 89 18 108 42 85 2 5 51 22 26 56 7 116 3 9 32 RAZ104 114 106 48 91 14 RAZ168 0.00 1000 1200 1400 1600 1800 2000 2200 2400 2600 2800 Yield (Kg/Ha) 19
  • 20. Activity 3: SNPs for bruchid resistance APA: Arcelin-Phytohemagglutinin-amylase Inhibitor family kb BAC: 71F18, Kami et al, 2006BAC wild mesoBAT93 mesoG19833 andean 20
  • 21. Precision introgression• Bruchid resistance (arcelin gene) originates from mesoamerican pool negative Positive Positive negative marker marker marker marker 1cM 1cM R locus The perfect marker is four markers• 4 markers easily available between genepools 21
  • 22. Activity 3: MAS for biotic traitsBGYMV (bean golden yellowmosaic virus):SCAR for bgm-1, but occasionalrecombinants (14 crosses) Recessive bc-3 resistance for BCMNV (bean common mosaic necrotic virus) (64 crosses) 22
  • 23. bc-3 candidate gene: eIF4ENADERPOUR et al. MOLECULAR PLANT PATHOLOGY (2010) C-A r r r r r r r r s s 1000 bp 820 bp 180 bp 23
  • 24. Common Bacterial Blight (CBB) MAS withBacterial blight: • SU91 on Chr8 (Pedraza et al. Xanthomonas 1997) • SCAR’s : BC420 on Chr6 (Yu et al. 1998) • SAP6 on Chr10 (Miklas et al. 2006) . 24
  • 25. CBB resistance QTLs Chr 8 Chr 10Map size : 166.82 cM Map size : 117.59 cM 0 BMbS15 10 12 14 16 18 20 22 24 26 28 30 10 2 4 6 8 4 6 8 0 0 1 2 3 BMbS13 BM212 0 3 SUcat01 BMbS12A Xc Xf 5 BMbS5 9 SU91 R2 =49% 21 BMd42 SUag01 12 gVQ 13 BMbS10 38 PV158 15 BMbS4 47 PV181 40 BMb1196w 51 PV185 SAP6 Xc 55 60 BMa27 R2 =20% 78 BM151 83 BMb386 86 BMb277 94 PVBR173 93 BMb96 102 BMc63 109 IAC54 111 BMc121 111 BMb302 113 BMb167 118 BMc66 141 PVBR71 Xc 167 BMb1319w Xf 25
  • 26. Activity 4: Drought tolerant traits• 36 advanced lines characterized (milestone 6)• Drought trials in – 2 saison in CIAT (2010, 2011), Palmira, ±drought – 1 saison in Ethiopia, ±drought• 3 visual scales for wilting, podfilling and degree of leaf loss analyzed (milestone 7) 26
  • 27. Relationship between irrigated and rainfed grain yield of 36 common bean genotypes grown under field conditions at CIAT-Colombia 1200 DAB 295 Rainfed grain yield (kg ha-1) DAB 489 DAB 528 DAB 494 1000 DAB 261 DAB 441 DAB 395 Mean: 798 DAB 557 DAB 541 DAB 525 LSD0.05: 383 DAB 520 DAB 555 DAB 545 800 DAB 318 DAB 432 DAB 353 DAB 317 DAB 302 DAB 344 DAB 380 DAB 530 600 KATB 1 AFR 298 DAB 564 DAB 493 CAL 143 400 CAL 96 Mean: 2934 LSD0.05: 565 200 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 Irrigated grain yield (kg ha-1) 27
  • 28. Activity 4: Visual scales Resistance to Wilting 28
  • 29. Relationship between leaf wilting and rainfed grain yield of 36 common bean genotypes grown under field conditions at CIAT-Colombia 1200 r = -0.36*** DAB 295 Rainfed grain yield (kg ha-1) DAB 494 DAB 528 DAB 489 DAB 441 1000 DAB 261 DAB 395 DAB 504 DAB 326 DAB 534 DAB 532 DAB 557 Mean: 798 DAB 545 DAB 514 LSD0.05: 383 DAB 520 DAB 555 800 DAB 290 DAB 432 DAB 353 DAB 318 DAB 317 DAB 302 DAB 380 DAB 344 DAB 530 600 AFR 298 KATB 1 DAB 564 DAB 493 CAL 143 400 CAL 96 Mean: 18.9 LSD0.05: 8.6 200 5 10 15 20 25 30 35 Wilting score at 41 days after plantingAdapted from King et al. 2009 Crop Science 49:290-298;0 = no wilting and 100 = plant death 29
  • 30. Relationship between seed filling and rainfed grain yield of36 common bean genotypes grown under field conditions 1200 at CIAT-Colombia DAB 295 DAB 489 r = -0.47*** Rainfed grain yield (kg ha-1) DAB 494 DAB 528 DAB 441 1000 DAB 261 DAB 395 DAB 534 DAB 504 DAB 532 DAB 557 DAB 525 DAB 549 DAB 520 DAB 555 DAB 545 800 Mean: 798 DAB 290 DAB 318 DAB 432 DAB 286 LSD0.05: 383 DAB 353 DAB 317 DAB 530 DAB 302 DAB 344 DAB 380 600 KATB 1 DAB 564 DAB 493 AFR 298 CAL 143 CAL 96 400 Mean: 4.78 LSD0.05: 2.0 200 2 3 4 5 6 7 Rainfed seed fill score 0 = well-filled grain; 10 = more than 50% of grain is not well-filled 30
  • 31. Conclusions• SNPs used in QTL and association mapping• MARS moving forward – Seed DNA extraction permits flexibility• MAS for biotic stress in implementation, moving toward routine• Advanced lines show improved yield• Visual scale of pod filling useful 31
  • 32. Thank you for your attention! 32