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Characterization and Mapping of Oat Crown Rust Resistance

This study focuses on the qualitative and quantitative characterization and mapping of oat crown rust resistance using phenotypic data from three assessment methods. Phenotypic reactions of the Ogle x TAM O-301 recombinant inbred line (RIL) population were analyzed for both single-gene and QTL mapping. The study also discusses the advantages of using quantitative PCR (qPCR) for mapping oat crown rust resistance.

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Characterization and Mapping of Oat Crown Rust Resistance

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  1. Qualitative and Quantitative Characterization and Mapping of Oat Crown Rust Resistance Using Phenotypic Data from Three Assessment Methods E. W. Jackson, D. E. Obert, M. Menz, G. Hu, J. B. Avant, J. Chong, and J. M. Bonman USDA-ARS Small Grains and Potato Germplasm Research Unit Aberdeen, ID

  2. CHARACTERIZATION ANDMAPPING Ogle x TAM O-301 recombinant inbred line (RIL) population 1. Single-gene a. Phenotype population based parental reactions (DLA and FDNA) b. Conversion into a phenotypic marker c. Analyze for linkage between phenotypic marker and genotypic markers (Mapmaker EXP/3.0) 2. QTL a. Phenotype population (DLA, FDNA) b. Analyze data for QTLs using a genetic linkage map and genotypic marker data (WinQTL Cartographer)

  3. PHENOTYPIC REACTIONS Greenhouse Field

  4. DISEASE ASSESSMENT Peterson et al., 1948 Lamari, 2002

  5. 100bp DISEASE ASSESSMENT 6 ◊ Puccinia coronata f.sp. avenae DNA □ P. graminis f.sp. avenae DNA ○ P. triticina DNA 5 4 ΔRn 3 2 1 0 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 -1 Cycle Number 300bp Oat P. Coronata isolates 300bp 200bp 200bp 100bp 100bp

  6. S S S S S S S S O O N N N N O O y = -3.5 (0.1)x + 34.9 (0.7), R2=0.997 (0.0004)

  7. Mean cycle threshold values (Ct) and standard deviations (SD) for the four standards used to estimate fungal DNA within plates for each test.

  8. 3.0 5.7 10.9 1.5 4.0 10.1 4.2 12.4 45.3 4.8 10.3 19.5 Severity of crown rust infection of parents Ogle and TAM O-301 measured using three different methods after inoculation with Puccinia coronata isolate CR185 in field and greenhouse experiments.

  9. Goodness-of-fit of crown rust resistant and susceptible Ogle x TAM-O-301 F6:8 RIL’s to a single gene model screened in the field (n = 4 reps) and greenhouse using three methods of assessment.

  10. OT6 KO13 CDO470B BCD1532 17.0 20.9 BCD855 BCD1235C 0.7 KO 13 Xbcd1532B UMN706B 20.9 17.7 Xumn706B 28.2 C (Xbcd1443B, Xisu2064B) 17.7 PC54 6.3 8.9 6.3 Xcdo460A 6.1 PcC CDO460A Xcdo1435B 4.0 (Xcdo549B) PSR598 1.9 Xumn107B Xumn706C 1.5 6.1 Xumn133B 2.0 (Xcdo1327, Xbcd876) CDO1435B Xcdo638 8.8 5.9 4.0 CDO640A, ISU54B Xbcd1876 5.9 1.4 UMN107B RZ543, CDO460B 1.5 Xcdo585B 0.4 Xbcd1154 1.9 1.5 2.0 UMN706C Xcdo1174B 2.4 (Xbcd1495, Xbcd1127B) UN133B 6.8 Xog49 CDO638 PcQ O’Donoughue, et al. unpublished PcD 5.9 BCD1876 PcV 5.9 25.7 CDO585B 1.5 0.4 2.4 BCD1154 CDO1174B Og49 e35061-2380 Bush and Wise, 1996

  11. Mean map positions to RFLP probe RZ543 of a candidate crown rust resistance gene in ‘Ogle’ based on three different assessments of Ogle x TAM-O-301 F6:8 RIL’s inoculated with Puccinia coronata isolate IA 189 in both field and greenhouse experiments (n = 4 reps).

  12. OT2 OT6 OT32 A03.875 CDO470B PSR637 0.2 Pc58a 4.1 PSR160B 3.1 12.1 CDO545B 17.0 qPCR Gh/Fd e35m61-101.0 6.0 BCD1235D BCD855 BCD1087 BCD1235C 1.1 0.7 29.6 3.1 10.2 Skdh 3.9 ISU77D 3.9 1.5 CDO1373A e35m61-122.t 28.2 BCD349 2.2 A04.360 5.4 10.7 visual Gh/Fd Adh2C digital Gh/Fd visual Gh/Fd CDO595 4.3 ISU136E PSR598 4.2 e40m48-2242.0 4.4 25.0 14.3 3.7 8.8 qPCR Fd qPCR Gh/Fd A17.350 CDO640A, ISU54B 4.1 0.8 1.1 1.1 0.6 0.7 3.5 1.4 11.0 RZ543, CDO460B CDO407 Pgd2 4.5 3.3 CDO1467A CDO1090C 3.4 6.8 RZ516A 35.0 PcQ RZ143Z PcD PSR547 12.6 BCD1280B PcV Acp2 ISU107B 15.0 25.7 7.0 CDO395 CDO949 1.7 CDO216D, PIC20B 5.1 PSR167 e35061-2380 * *

  13. KO4 KO4 CDO220 CDO220 4.3 4.3 5.6 8.3 8.9 5.2 2.1 1.2 1.6 12.0 CDO618A CDO618A 5.6 CDO580 CDO580 8.3 CDO718B CDO718B 8.9 CDO309A CDO309A 5.2 UMN341A UMN341A UMN101 UMN282 UMN214A 2.1 1.2 1.6 3.0 9.0 15.0 UMN101 UMN282 UMN214A PcA PC59 6.3 Awn-A Avn-A Bush and Wise, 1996 PcB O’Donoughue, et al. unpublished OT11 CDO580 3.1 CDO216F 1.1 RZ574B 1.5 BCD1823A 43.6 CDO244 39.8 qPCR Fd/Gh Idh * 8.0 1.7 CDO328 3.6 BCD828A 4.7 RZ444B 14.4 PIC20A

  14. CONCLUSIONS • I. Single-gene analysis • Major gene conferring resistance to P. coronata isolate CR185 (race NBFB) in Ogle, which mapped to OT6. • Resistance on KO13 • Bush and Wise, 1996 • O’Donoughue et al, unpublished • II. QTL analysis • Major QTL on OT6 using all 3 assessments (Ogle) • Minor QTL on OT32 using visual and q-PCR (TAM O-301) • Minor QTL on OT2 using q-PCR (TAM O-301) • Candidate QTL on OT11 using q-PCR (Ogle) • III. Advantages of qPCR • Resolution • Differences between Ogle and TAM O-301 • Mapping precision • Placement of the single gene • Two-point linkage vs. QTL on OT6 • Mapping resolution • Higher LOD score on OT6 and tighter QTL intervals • Two additional QTLs resolved on OT2 and OT11

  15. ONGOING WORK Noble-2 MN841801-1 Makuru MN841801-1

  16. OT11 CDO580 3.1 CDO216F 1.1 RZ574B 1.5 BCD1823A PSR129B 4.1 PcMN111 3.2 RZ682B 1.9 OT33 D ISU77A 4.3 OISU2192b 1.3 39.5 RZ516c 3.4 RZ516d 4.6 Pc58b CDO244 37.6 39.8 qPCR Fd/Gh Idh * 8.0 1.7 Pc58c CDO328 3.1 3.6 BCD828A PSR637 0.3 4.7 RZ444B Pc58a 4.5 OT32 PSR160B 14.4 3.6 D CDO545B PIC20A OT32 / 33 Hoffman et al. In press, Crop Science

  17. AKNOWLEDGEMENTS Coauthors, Dr. Monica Menz, Dr. James Chong, Dr. Don Obert, Dr. Mike Bonman, and Mrs. Jana Avant Mrs. Kathy Satterfield, Mrs. Irene Shackelford, Mrs. Rebeca Caldera USDA-ARS NSG&PR NSGC Aberdeen, ID

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