Samuel F. Hutton

Transcription

1 Samuel F. Hutton

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4 Vectored by thrips (various spp.) Tomato chlorotic spot virus (TCSV) Groundnut ring spot virus (GRSV) Tomato spotted wilt virus (TSWV)

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6 7482B 8516 F 4 CK12 F B 7482 F Disease screens F 1 S. chilense LA1938 Spring 2002: Spring 2004: Spring 2005: (7482B x CK12) F 2 grown in Quincy. 5 selections [no TSWV] F 3 lines evaluated in Quincy. 7 selections Seven F 4 lines evaluated in S. Georgia.

7 Tomato spotted wilt disease incidence for seven lines derived from S. chilense LA1938 and control hybrids grown in South Georgia, Spring 2005 plus Chisquare test for goodness of fit to a single dominant gene model. Genotype Conclusion y No. Plants Total Healthy Diseased (%) z Chisquare (3:1) (29) Seg (8516B) (0.8) R 9-3 (8516) (0.8) R (69) S (28) Seg (8516C) (0.8) R (34) Seg Crista (Sw-5) (1.5) R - control Mt. Spring (57) S - control z There was an average of 63% infection for the 2 susceptible genotypes 9-4 and Mt. Spring. y R = resistant, Seg = segregating, S = susceptible. P

8 Fla. 8516

9 Fall 2005: Fla crossed with 21 parent lines Spring 2006: 18 F 1 s advanced to F 2 Fall 2006: Spring 2007: 102 F 2 plants selected [no TSWV infection] F 3 lines and controls field tested for TSWV Sw-7 location reported on chr 12 (Stevens et al TBRT. (Dockter et al HortScience 44:1123) 3.8 Mb Whole genome re-sequencing of Fla confirms S. chilense chr 12 introgression

10 Tomato spotted wilt virus incidence for controls and 102 F 3 lines varying for the Sw-7 introgression on chromosome 12, tested in Quincy, FL, Spring Line Genotype No. Plants TSWV (%) Fla R control 29 3 c Tasti-Lee S control a F 3 lines: 18 lines Hom. Sw bc 60 lines Segregating b 24 lines Hom. susceptible a z Mean separation in columns by Duncan-Waller k ratio t test at P <0.05.

11 Backcross of resistant lines from Quincy 2007 trial Screen F 2 s for recombination within chromosome 12 introgression # recombinants [7776 x (7776 x 8516)] 4 [7777 x (7777 x 8516)] 30 [8021 x (8021 x 8516)] 1 [8022B x (8022 x 8516)] 1 [8111B x (8111B x 8516)] 16 [8249 x (8249 x 8516)] 13 Evaluate recombinant inbred lines (RILs) in the field Quincy, FL (2011, 2012, 2013) Hawaii (2014)

12 Markers Quincy RIL Hawaii 2014 Infection Rate % % 61-80% % 1-20% 0% derived Susc. - derived

13 Markers Quincy RIL Hawaii 2014 Infection Rate % % 61-80% % 1-20% 0% derived Susc. - derived

14 Tomato spotted wilt virus disease incidence for control lines grown in Hawaii, Line Gene TSWV (%) Fla Susc. 100 a z (8736 x 8820) Sw-7 / 95 a Fla Sw a Fla Sw a CK12 Sw-7 source 32 b Fla Sw-5 / 25 b Fla. 8124C Sw b z Mean separation in columns by Duncan-Waller k ratio t test at P <0.05.

15 Markers Quincy RIL Hawaii 2014 Infection Rate % % 61-80% % 1-20% 0% derived Susc. - derived

16 CT10953i CT100 P21 P36 P36 P *** 4.38*** P175*** P194 P217 TG360 CT99 T1736 Mega base pair (Mbp)

17 Tomato chlorotic spot virus (TCSV) Groundnut ring spot virus (GRSV)

18 Tomato chlorotic spot virus disease incidence in Sw-5 and Sw-7 genotypes, greenhouse study, Line Gene(s) Total No. No. Infected % Infection Florida Susc Fla Tribeca 14 0 Sw5 / Dixie Red Fla. 8124C 9 0 Sw Sw5 + Sw Sw

19 CK12 and 8516 screening Stevens, Scott, Olson Sw-7 RIL testing Olson Nunhems TCSV screens FDACS ( , ) Adkins, Turecheck, Funderburk

20 Tomato Mottle Virus (ToMoV) Tomato Yellow Leaf Curl Virus (TYLCV)

21 Transmitted by Sweetpotato Whitefly Bemisia tabaci (Genn.)

22 » Major focus at University of Florida since 1990» Resistance sources S. chilense LA 2779 S. chilense LA 1932 S. chilense LA 1938 S. lycopersicum cv. Tyking» Inoculations TYLCV presently ToMoV through 2006

23 Gene Species Chromosome Reference Ty-1 S. chilense 6 Zamir et al., 1994 Ty-2 S. habrochaites 11 Hanson et al., 2000 Ty-3 S. chilense 6 Ji et al., 2007 Ty-4 S. chilense 3 Ji et al., 2009 ty-5 S. lycopersicum (?) 4 Anbinder et al., 2009 Ty-6 S. chilense (?) 10 Hutton et al., 2014

24 Ty-3 Fine Mapping

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26 Ty-6 Mapping F 1 Fla Fla Chr 10» (Fla x Fla. 7776) F F2 plants TYLCV inoculation 156 polymorphic markers spanning 11 chr s Simple Interval Mapping» Single QTL on Chromosome 10» 59.4% phenotypic variance explained

27 Ty-6 Fine Mapping Chr 10» (Fla. 8503C x Fla. 7060) F F2 plants TYLCV 114 F2 plants ToMoV 46 proprietary markers Simple Interval Mapping TYLCV. ToMoV» Chromosome 10 confirmed 97.6% TYLCV variance explained 99.4% ToMoV variance explained

28 Top: Analysis of the (Fla and Fla. 7781) F 2 population tested in fall 2006 for effect of the Ty-3 and the Ty-6 loci against TYLCV. Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for Ty-3 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq Ty <0.0001*** Ty <0.0001*** Ty-3 Ty Ty-3 Ty-6 N Mean DSI RME 95% CI a / b c / c / / d / e f / g h

29 Top: Analysis of the (Fla and Fla. 7781) F 2 population tested in fall 2006 for effect of the Ty-3 and the Ty-6 loci against TYLCV. Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for Ty-3 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq Ty <0.0001*** Ty <0.0001*** Ty-3 Ty TYLCV DSI 4 3 Ty-3 Ty-6 N Mean DSI RME 95% CI a / b c / c / / d a b c / e /- +/- +/+ Ty-3 Genotype f / g h c d e f g h Ty-6 Genotype -/- +/- +/+

30 Top: Analysis of the (Fla. 8638B and Fla. 7987) F Need correct 2 population tested in fall 2012 for effect of the ty-5 and the Ty-6 loci against TYLCV. year Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for ty-5 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq ty <0.0001*** Ty <0.0001*** ty-5 Ty ty-5 Ty-6 N Mean DSI RME 95% CI a / b c / a / / b / c c / d e

31 Top: Analysis of the (Fla. 8638B and Fla. 7987) F Need correct 2 population tested in fall 2012 for effect of the ty-5 and the Ty-6 loci against TYLCV. year Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for ty-5 and the Ty-6 genotype combinations. a Num DF Den DF ChiSq F value Pr > ChiSq ty <0.0001*** Ty <0.0001*** ty-5 Ty TYLCV DSI 4 3 ty-5 Ty-6 N Mean DSI RME 95% CI a / b c / a / / b a b c / c /- +/- +/+ ty-5 Genotype c / d e a b c c d e Ty-6 Genotype -/- +/- +/+

32 Top: Analysis of the (Fla and Fla. 8472) F 2 population tested in spring 2013 for effect of the ty-5 and the Ty-6 loci against ToMoV. Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for ty-5 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq ty Ty *** ty-5 Ty ty-5 Ty-6 N Mean DSI RME 95% CI a / ab b / a / / ab / ab a / ab b

33 Top: Analysis of the (Fla and Fla. 8472) F 2 population tested in spring 2013 for effect of the ty-5 and the Ty-6 loci against ToMoV. Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for ty-5 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq ty Ty *** ty-5 Ty ToMoV DSI 3 2 ty-5 Ty-6 N Mean DSI RME 95% CI a / ab b / a / / ab a ab b / ab /- +/- +/+ ty-5 Genotype a / ab b a ab ab a ab b Ty-6 Genotype -/- +/- +/+

34 Tomato yellow leaf curl virus (TYLCV) and tomato mottle virus (ToMoV) disease severity z for tomato genotypes inoculated at the seedling stage at GCREC, spring Genotype Begomovirus resistance gene TYLCV ToMoV Horizon a y 3.3 b Fla Ty b 0.8 d Tygress Ty-1/+ 1.8 b 3.0 bc Fla. 8638B Ty-6, ty c 0.9 d Fla Ty b 2.7 c Fla Ty-3, Ty c 0.1 d TAMU 5 Ty d 3.9 a z Rated at 66 days after inoculation began on a 0-4 scale where lower number indicated less disease. For scale and inoculation information see Hutton et al y Mean separation in columns by Duncan s multiple range test at P < 0.05.

35 Ty-6 Fine Mapping Chr 10» (Fla. 8503C x Fla. 7060) F F2 plants TYLCV 114 F2 plants ToMoV 46 proprietary markers Simple Interval Mapping TYLCV. ToMoV» Chromosome 10 confirmed 97.6% TYLCV variance explained 99.4% ToMoV variance explained

36 snp417 sl_61192 Ty6QTL-264 Ty6QTL-155 sl_61131 sl_61108 Ty6QTL-267 Ty6QTL-268 CL sl_61027 sl_8855 Ty6QTL-166 sl_60980 Ty6QTL-169 sl_8835 Ty6QTL-279 sl_15094 sl_8774 Germplasm Marker Physical position Ty-6 Fla AA AA GG GG GG GG CC CC TT AA AA TT CC GG AA TT GG CC Fla AA AA GG GG GG GG TT AA AA TT CC GG AA -- AA CC Fla GG AA GG GG GG GG CC CC TT -- AA TT CC GG GG TT GG CC Fla AA AG CC AA AG AG TT AA CC TT CC CC TT AA GG TT GG AA Fla AA AA GG GG GG GG TT AA TT AA AA TT CC GG AA CC AA CC Fla. 8638b + AA GG GG GG GG GG CC CC TT TT CC CC TT GG GG TT GG CC Fla. 8503C + GG TT GG GG AA AA TT AA TT AA CC TT CC GG GG CC GG CC Fla. 8472B + CC CC CC AA TT AA TT AA TT TT TT CC TT AA AA TT AA TT Fla GG TT GG GG AA CC CC CC -- AA TT TT CC GG GG TT GG CC Fla GG GG CC -- AA AA TT AA CC TT CC CC TT AA GG TT GG AA Fla GG GG CC AA AA AA TT AA CC TT CC CC TT AA GG TT GG CC Fla GG GG CC AA AA AA TT AA CC TT CC CC TT AA GG TT GG CC Fla GG GG GG GG AA AA -- AA CC AA CC TT CC GG GG CC GG AA Fla GG GG CC AA AA AA TT AA TT TT AA TT CC GG GG TT GG CC Fla GG GG CC -- AA AA -- AA CC TT CC CC TT AA GG TT GG CC Fla GG GG CC AA AA AA TT AA CC TT CC TT CC GG GG TT GG CC

37 Ty-6 Fine Mapping E901 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X 1 Y:Y Y:Y 1 S 4 E902 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X Y:Y 1 Y:Y Y:Y 1 S 4 E929 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X Y:Y Y:Y 2 Y:Y Y:Y 2 S 4 E930 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 1 0 X:X Y:Y Y:Y Y:Y 2 Y:Y Y:Y 2 S 4 E936 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 Y:Y Y:Y Y:Y Y:Y 2 Y:Y Y:Y 2 S 4 E932 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 2 Y:Y Y:Y Y:Y Y:Y 2 Y:Y Y:Y 2 S 4 E934 X:X X:X X:X X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 2 2 Y:Y Y:Y Y:Y Y:Y 2 Y:Y Y:Y 2 S 4 E914 X:X X:X X:X X:X X:X Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 2 Y:Y Y:Y Y:Y Y:Y 1 Y:Y X:X 0 R 2 E937 X:X X:X Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 2 Y:Y Y:Y Y:Y Y:Y 2 Y:Y Y:Y 2 R 2 E916 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 2 Y:Y Y:Y X:X X:X 0 X:X X:X 0 R 2 E918 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 2 Y:Y X:X X:X X:X 0 X:X X:X 0 R 2 E923 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 2 X:X X:X X:X X:X 0 X:X X:X - R 2 E920 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 2 0 X:X X:X X:X X:X 0 X:X X:X 0 R 2 E921 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 2 Y:Y 2 2 Y:Y Y:Y 0 0 X:X X:X X:X X:X 0 X:X X:X 0 R 1.5 E944 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X 1 X:X X:X 1 S 4 E945 Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y Y:Y X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X Y:Y X:X X:X 1 X:X X:X 1 S 4 E946 Y:Y Y:Y Y:Y Y:Y Y:Y X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X X:X X:X 1 S 4 E947 Y:Y Y:Y Y:Y Y:Y X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X 1 X:X X:X 1 S 4 E948 Y:Y Y:Y Y:Y X:X X:X X:X X:X X:X X:X X:X 0 X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X 1 X:X - - S 4 E926 Y:Y Y:Y X:X X:X X:X X:X X:X X:X X:X X:X - X:X 0 0 X:X X:X 0 0 X:X X:X X:X X:X 0 X:X X:X 0 S 4 89 Kb E914 X:Y X:Y X:Y X:Y S 4 E931 Y:Y Y:Y X:Y X:Y X:Y S 4 E930 X:Y X:Y X:Y X:Y S 4 E934 X:X X:X X:X 0 X:X X:X 2 S 3.8 E947 Y:Y Y:Y Y:Y Y:Y Y:Y R 1.8 E922 Y:Y Y:Y Y:Y 2 Y:Y Y:Y 0 R 1.9 E923 X:X X:X X:Y X:Y? R 1.7 E921 X:Y X:Y X:Y X:X X:X S 4 E944 Y:Y X:X X:X 0 X:X X:X 0 S Kb Intergenic Intron 1 Exon 13 Intron 13 Intergenic Gene 1 Gene 2 Gene 3

38 ToMV Tm-2 2 primary source of resistance Risk of spread of breaking strains TSWV Sw-5 primary gene for resistance; still effective in most areas Sw-7 effective under low-moderate pressure, weaker than Sw-5 Sw-7 effective against Sw-5-breaking strains (??); not against TCSV Cannot screen by mechanical inoculation (MAS essential) Fine-mapped to ~140 Kb interval; markers available Begomoviruses Ty-1/3 widely used ty-5 recessive; ty-5 and Ty-2 ineffective against some viruses Ty-6 most effective to ToMoV; combine with Ty-1/3 for high, durable resistance Ty-6 fine mapped to ~55 Kb interval; markers available

39 Tomato Breeding Lab Upinder Gill John Smeda Reza Shekasteband Dolly Cummings Tim Davis Keri Druffel Jose Diaz Kazuyo Ueda Nate Brown Judith Lopez Leticia Kumar Rebecca Wente Jessica Chitwood Jasmine Lopez Edgar Sierra

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41 Top: Analysis of the (Fla and Fla. 8062) F 2 population tested in spring 2013 for effect of the ty-5 and the Ty-6 loci against ToMoV. Bottom: Mean disease severity index (DSI) and relative marginal effect (RME) for ty-5 and the Ty-6 genotype combinations. Num DF Den DF ChiSq F value Pr > ChiSq ty Ty <0.0001*** ty-5 Ty ty-5 Ty-6 N Mean DSI RME 95% CI a / b c / ab / / ab / ac ab / ab c

42 ToMoV DSI Ty-6 Genotype -/- +/- +/ /- +/- +/+ ty-5 Genotype