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ARM 2008: Dissection, characterisation and utilisation of disease QTL -- R Nelson

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ARM 2008: Dissection, characterisation and utilisation of disease QTL -- R Nelson

  1. 1. Indonesia - Bustamam - Utut KARI - Gethi Cornell Dissection, characterization and utilization of disease QTL IRRI - Vera Cruz - Leung - Brar CSU - Leach - Nelson - Smith NCSU - Balint-Kurti Rice Maize Generation Challenge Program Project #8 Update 2008
  2. 2. 5 6 7 8 9 10 9 8 7 6 5 Gray Leaf Spot E-MBLUP Northern Leaf Blight E-MBLUP disease GLS NLB SLB ***0.61 ***0.62 GLS - ***0.45 SLB a: Unknown gene b: tasselseed2 c: Glutathione S-Transferase 4 GLS NLB 3 2 1 Randy Wisser 1 2 3 4 5 6 7 8 9 1 2 3 4 0 Southern Leaf Blight E-MBLUP E E Association mapping population (Buckler; n=~300): 11 datasets for three diseases -0.4 -0.2 0.0 0.2 0.4 0.6 0.8 1.0 allele effect a b c { { {
  3. 3. QTL identified in NAM for NLB , SLB and GLS 0 QTL identified in NAM for NLB , SLB and GLS -1 -2 -3 -4 -5 Nested association mapping population (Buckler et al.; n=5,000): 6 datasets for 3 diseases FLECKS -6 -7 -8 -9 -10 SLB NLB GLS 12 of 13 NLB-QTL in full NAM analysis are present both years K. Kump/PBK et al., NCSU; J. Poland and J. Benson/RJN et al., CU
  4. 4. 9 8 7 6 5 AUDPC Gray Leaf Spot: Allele effects at qCz4.06 6 alleles? 24 22 20 18 16 14 12 10 8 6 4 LSmean Diseased Leaf Area (%) Northern Leaf Blight: Allele effects at qEt8.06 Parental Allele 3 alleles?
  5. 5. Near-isogenic lines Crop/lab Developer Source Background Target No. lines Rice / HL, JL Leung, Leac h Deletion library IR64 Whole genome n=12 char. Rice / HL Leung SH2-2 TX2-13 (HIF) Chr. 6, 9 n=13 Rice / Bustamam, OL5 Way Rarem Chr. 6, 9 n=2 CMVC, MB Vera Cruz RRiiccee // CCMMVVCC MMoorroobbrrkknn VVaannddaannaa nn==77 nn==6600 Maize / PBK Zwonitzer NC250 B73 n=12 n=137 Maize / RJN Chung Tx303 B73 1.02, 1.06 n=17 Maize / RJN Chung CML52 B73 (HIF) n=9 n=46 Maize / RJN Chung DK888 S11 (HIF) n=5 n=23 Maize / JG Gethi TZMi102, TZMi711, TZMi712, CML384, CML312. CML 204, CML 373 (HIF) Whole genome n=72
  6. 6. NLB: histopathology Field Infection efficiency (2 days after inoculation) 0 0.2 0.4 0.6 0.8 1 Tx3 03 B73 Maize genotype TBBC3_38_05F T BBC 3_42 _10E _2 I n f e c ti o n e ffi c i e n c y (s u c c e s s f u l in f e c t io n / g e rm in a t e d c o n id ia ) Tx303 allele at the NLB QTL in bin 1.06 QTL x E reduces fungal penetration SLB: Field Growth Chamber Incidence of E. turcicum growing into the xylem (4 days after inoculation) 0 0.1 0.2 0.3 0.4 0.5 0.6 Tx303 B73 Maize genotype TBBC3_38_05F TBBC3_42_10E_2 Incidence (hyphae in xylem / infection site) B73 allele at the NLB QTL in bin 1.02 More robust relative to reduces fungal colonization environments? of the vasculature
  7. 7. QTL isolines with impressive phenotypic effects in the field + QTL – chr. 6 - QTL – chr. 6 + QTL – 1.02 - QTL – 1.02
  8. 8. A. flavus biomass estimated by Quantitative Real-Time PCR is strongly correlated with aflatoxin concentration 4 3 2 1 0 log Infection Coefficient 2 3 4 5 6 7 8 log (ppb+1) A. flavus Infection Coefficient (log IC) Aflatoxin Concentration (log ppb) Pearson correlation == 00..8855**** nn==2200 QTL mapping for silk and young kernel resistance to colonization • CML322 x B73 RILs • Tx303 NILs (B73 background) Bin 7.02-7.03 • CML52 HIFs (B73) Bin 6.05 To be confirmed with 2008 field data (analysis in progress) S. Mideros, Cornell
  9. 9. MDR varieties in release process in Kenya Test Code Pedigree Region Tons Ha-1 MTPEH200805 TZMi 712/CML 373//CML 312 Coastal lowlands 7.0 KATEH200804 TZMi 102/CML 373//CML 312 Drylands 9.6 MTPEH200801 CML 373/TZMi 711//CML 312 Coastal lowlands 8.9 KATEH200803 CML 373/TZMi 711//CML 312 Drylands 9.3 MTPEH200803 CML 373/TZMi 102//CML 312 Coastal lowlands 7.6 MTPEH200802 CML 204/TZMi 711//CML 312 Coastal lowlands 8.8 MTPEH200804 CML 204/TZMi 102//CML 312 Coastal lowlands 7.1 KATEH200802 CML 204/TZMi 102//CML 312 Drylands 9.6 KATEH200801 CML 204/CML 373//CML 312 Drylands 10.0 J. Gethi, KARI
  10. 10. Vandana/Moroberekan-derived BC3F8 intermated lines for multilocation trials in India, 2008 NAME Yield (g) Yield (g) Seedling blast (0-9) % DLA PBS (0-9) Neckblast (%) Seedling blast (0-9) Candidate Gene(s) Almora IRRI IRRI (50DAS) IRRI Almora Cavinti Hazaribag Grain Length Grain Shape Grain Quality Analysis Chalkiness (0-none, 9-large) Gelatinization Temperature Amylose Content (%) Aroma IR78221-19-3-196-B-B (Susceptible control) 100 5.0 85.0 4.0 57.5 8.25 10.0 4.0 CHI 5 5 9 HI/I 24.5 slight 90 IR78221-19-4-54-B-B 152.5 68.5 1.0 1.5 3.55 51.3 2.0 CHI,OXO THAU7, POX OXLP 3 1 9 HI/I 25.4 slight 80 IR78221-19-6-7-B-B 153.5 90.4 1.0 1.0 3.25 20.8 1.0 OXO, HSP90 POX 3 1 9 I 24.7 none 70 Mean % diseased leaf area IR78221-19-6-33-B-B 105.0 94.8 1.0 2.0 3.95 2.4 1.5 OXO, POX OXLP 60 50 40 30 20 10 chitinase, oxalate oxidase, thaumatin, peroxidase, oxalate oxidase-like protein oxalate Traits of the advanced elite lines: • blast resistance based on early generation multi-location testing • morpho-agronomic traits comparable to Vandana • presence of candidate genes associated with blast resistance • yield comparable to Vandana under low rainfall during reproductive stage 5 5 1 I 25.5 none IR78221-19-6-56-B-B 80.0 134.8 1.0 1.0 3.1 1.3 1.5 CHI, OXO HSP90, POX 3 1 9 I 25.3 none IR78221-19-6-82-B-B 165.0 70.0 1.0 1.0 3.4 7.5 1.0 OXO, POX OXLP, PR10 3 1 5 I 25.6 none IR78221-19-6-90-B-B 112.5 108.5 1.0 1.0 3.0 5.0 4.0 OXO, POX OXLP 3 1 0 I 25.2 slight IR78221-19-6-99-B-B 170.0 109.5 1.0 1.0 3.3 10.2 1.5 OXO 3 1 1 I 24.8 none IR78222-20-7-148-2-B 70.0 128.5 4.0 1.5 5.15 3.0 0.0 CHI, OXO OXLP, DHAP 5 5 5 HI/I 20.2 slight 0 196 54 7 33 56 82 90 99 2 IR64 BC3F8 VxM intermated lines* oxidase
  11. 11. Deliverables over project lifetime • Understanding the trait • Dissecting the trait – QTL syntheses: published – Selection mapping: published – Deletion mapping by dot-blot & microarray: pub. & submitted – Large-scale QTL analyses • SLB, NLB and GLS – Sets of QTL NILs (maize, rice) – Deletions in 14 rice mutants – Association analysis for MDR: in mapped preparation – Phylogenomics of candidate genes – Win-win and win-lose QTL • Improving the trait – QTL characterization – Histopathology – Fine-mapping in progress for several QTL in maize – Maize lines with MDR in advanced trials in Kenya – Disease resistant elite rice lines in India and Indonesia

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