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. 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) C HARACTERIZATION AND MAPPING

3. GreenhouseField P HENOTYPIC REACTIONS

4. D ISEASE ASSESSMENT Peterson et al., 1948 Lamari, 2002

5. 100bp 300bp 200bp 100bp 300bp 200bp 100bp P. Coronata isolates Oat D ISEASE ASSESSMENT

6. y = -3.5 (0.1)x + 34.9 (0.7), R 2 =0.997 (0.0004) S O N S S SS S S S OO O NN N

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. 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. 4.2 12.4 45.3 4.8 10.3 19.5 3.0 5.7 10.9 1.5 4.0 10.1

9. Goodness-of-fit of crown rust resistant and susceptible Ogle x TAM-O-301 F 6:8 RIL’s to a single gene model screened in the field (n = 4 reps) and greenhouse using three methods of assessment.

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 unpublished BCD1532 UMN706B CDO460A CDO1435B UMN107B UMN706C UN133B CDO638 BCD1876 CDO585B BCD1154 CDO1174B Og49 20.9 17.7 6.1 4.0 1.9 1.5 2.0 5.9 1.5 0.4 2.4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

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 F 6:8 RIL’s inoculated with Puccinia coronata isolate IA 189 in both field and greenhouse experiments (n = 4 reps).

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

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 unpublished CDO220 CDO618A CDO580 CDO718B CDO309A UMN341A UMN101 UMN282 UMN214A Avn-A 4.3 5.6 8.3 8.9 5.2 2.1 1.2 1.6 12.0 PC59 6.3 KO4 Bush and Wise, 1996 1.7 qPCR Fd/Gh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

14. C ONCLUSIONS I. Single-gene analysis 1.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 1.Resolution  Differences between Ogle and TAM O-301 2.Mapping precision  Placement of the single gene  Two-point linkage vs. QTL on OT6 3.Mapping resolution  Higher LOD score on OT6 and tighter QTL intervals  Two additional QTLs resolved on OT2 and OT11

15. Noble-2MN841801-1 Makuru O NGOING WORK

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

17. A KNOWLEDGEMENTS 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