Bacterial spot of tomato, race T4: Identification of QTL associated

with resistance

Sam Hutton, Jay ScottUniversity of Florida, GCREC, 14625 CR 672, Wimauma, FL

(email: sfhutton@ufl.edu; jwsc@ufl.edu)

Bacterial Spot

• Causal agent:– Xanthomonas euvesicatoria (Race T1)– Xanthomonas vesicatoria (Race T2)– Xanthomonas perforans (Races T3, T4, T5)

T4 Partial Resistance

PI 126932(S. pimpinellifolium)

(Low R)

PI 128216(S. pimpinellifolium)

(Mod R)

PI 114490(S. lycopersicon)

(Good R)

Fla 8326(Mod R)

Fla 8233(Mod-Good R)

Fla 8517(Mod-Good R)

Fla 7776 moderately susceptibleFla 7946 highly susceptible

H7998 H7998H7998

T3 HRT3 HR++ T3 HRT3 HR++ T3 HRT3 HR++

Fla. 7776

Fla. 7946

PI 114490

Fla. 8517

Fla. 8233

H7998

OH 9242

4099

Inheritance

• Generation Means Analyses (Field Experiments)

8326• Fall ’05• Spring ’06• Summer ’07

8233• Spring ’07

8517• Summer ’07

Mather-Jinks Summary

• Similar results among 8233, 8517 and 8326 studies

• Intermediate F1 resistance levels– Only partial resistance

• Effects– Dominance important– Epistatic interactions (duplicate dominance)– Some additive

Molecular Markers

• Resistant breeding lines screened with polymorphic markers to identify regions of possible introgression

• Selective Genotyping:

– R and S selections made from the F2 generation of each:• 8326 x 7946• 8233 x 7776• 8517 x 7776

– Within each family:• Each polymorphic marker analyzed for Transmission Disequillibrium

(George, et al., 1999; Zhu and Elston, 2001)

Molecular Markers

• Resistant breeding lines screened with polymorphic markers to identify regions of possible introgression

• Selective Genotyping:

– R and S selections made from the F2 generation of each:• 8326 x 7946• 8233 x 7776• 8517 x 7776

– Within each family:• Each polymorphic marker analyzed for Transmission Disequillibrium

(George, et al., 1999; Zhu and Elston, 2001)

Chr 12

Chr 2 Chr 3 Chr 4 Chr 5 Chr 6

Chr 7 Chr 9Chr 8 Chr 10

Chr 1

Chr 11

Fla. 8326

H7998 PI 126932 undetermined

P = 0.063

P = 0.000

P = 0.044

Chr 12

Chr 2 Chr 3 Chr 4 Chr 5 Chr 6

Chr 7 Chr 9Chr 8 Chr 10

Chr 1

Chr 11

Fla. 8233

H7998 PI 128216 undetermined

P = 0.104P = 0.059

P = 0.104

P = 0.022

P = 0.022 P = 0.018

P = 0.005

P = 0.009

Chr 12

Chr 2 Chr 3 Chr 4 Chr 5 Chr 6

Chr 7 Chr 9Chr 8 Chr 10

Chr 1

Chr 11

Fla. 8517

OH9242 PI 114490 undeterminedPI 128216H7998

Marker Summary• Partial resistance in Florida breeding lines 8233, 8326, 8517

• 4 resistance QTL identified:– chr 3* PI 114490– chr 9* PI 128216– chr 11* H7998 / PI 128216– chr 12* non-OH9242

• 3 plausible QTL:– chr 1 PI 126932– chr 5 PI 128216– chr 10 PI 128216

• Fall 08 confirmation experiments…

Post Doc Days

www.bmooninc.com

Fall 08• Three F2 populations:

– 8233 x 8111– 8517 x 7946 (I-3 +)– 8326 x 7946 (I-3 +)

• Each plant rated forbacterial spot severity

• Each plant genotyped atcandidate loci

• Stepwise ANOVA

8233 x 8111 F2

• Candidate loci: Chromosomes 1 5 9 10 11

• Stepwise ANOVA:

Chr P11 <.0001

30 plants:15 +15 /

0 -

30 plants:1 +5 /24 -

3.44 6.10

• Candidate loci: Chromosomes 1 3 7 9 10 11

• Stepwise ANOVA:

Chr P7 (I-3) <.0001

11 <.0001

8326 x 7946 F2

1.19 0.54Average number of chr 11 R alleles:

0.28 1.46Average number of I-3 alleles:

3.96 6.72

• Candidate loci: Chromosomes 1 3 7 9 10 11 12

• Stepwise ANOVA:

Chr P11 <.00017 (I-3) <.00013 .009812 .0529

8517 x 7946 F2

0.33 0.64Average number OH9242 alleles:

1.10 0.93Average number of chr 3 R alleles:

2.00 6.33

(Rx-4) T3 HR

• Stepwise ANOVA:

Marker F Value PSL 10737i 52.4 <.0001C2 30825 157.4 <.0001

• Estimate of Effect:Genotype Time+ 26.5/ 36.6- 64.1

Chr 11

C2 10050 (54 cM)SL 10737i

C2 30825 (72 cM)

LEOH 57

C2 54470 (72 cM)

8517 Selective Genotyping

R S-+

C2 10050 (chromosome 11, 54 cM)

R S

I-3+I-3-

8517 Selective Genotyping

I-3 SCAR (D. Maxwell) What we’re up against: Developing material that is I-3+ and has R to bacterial spot.

0629 0630 0631

I-3- I-3-I-3+

7946 x 8517 selections:

0629 Severity Rating = 3

0630 Severity Rating = 2.5

0631 Severity Rating = 5.5

0629 0630 0631

I-3- I-3-I-3+

Chr 3: - + +Chr 11: + + -?Chr 12: + - -

Acknowledgements

• Advisor– Dr. Jay Scott

• UF Tomato Labs– Cathy Provenzano– Rosa Ayala– Rudy Jones– Jose Diaz– Dolly Cummings– Dr. Yuanfu Ji– Dr. Aliya Momotaz– Dr. Jeremy Edwards– Sarah Smith

• OSU Tomato Lab– Dr. David Francis– Dr. Matt Robbins– Dr. Sung-Chur Sim

• Committee Members– Dr. Jeff Jones– Dr. Harry Klee– Dr. Eileen Kabelka

• Other Scientists– Dr. Steven Mackenzie– Dr. Bob Stall– Dr. Garry Vallad– Jerry Minsavage

• Funding– Florida Tomato Committee