June 29, Tomato Genetics and Breeding at Penn State. An Overview. Majid R. Foolad
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1 June 29, 2009 Tomato Genetics and Breeding at Penn State An Overview Majid R. Foolad
2 OUTLINE Traits of Interest Genetic and Breeding Research Breeding Activities Fresh-market breeding lines Processing breeding lines
3 Major Traits of Interest Disease Resistance Early Blight Late Blight Fruit Quality Lycopene Other Traits Adaptation to NE conditions Yield Maturity (short and mid-season) Other traits
4 Early Blight (Alternaria solani and A. tomatophila)
5 Sources of EB Resistance in Tomato Genetic sources of resistance identified mainly in wild species S. habrochaites and S. pimpinellifolium Used a few accessions for genetics and breeding research Filial populations BC populations RIL populations
6 Nature of EB Resistance Does not follow the gene-for-gene interaction model No major resistance gene identified No pathogen race specificity identified It exhibits quantitative inheritance Low-to-moderate heritability Multiple genetic factors
7 EB-R QTLs in different S. lycopersicum x S. habrochaites BC populations EBR Chr1 CT197 (0.0) TG24 (4.8) AN (4.5) AN (0.0) XLRR.390 (0.0) TG70 (9.1) TG208b (4.4) TG223 (2.2) TG273 (16.9) TG460 (14.8) TG559 (15.6) TG208a (8.2) CT137 (15.3) EBR Chr2 PK PK (0.0) (0.9) CLRR.490 (1.4) XLRR.380 (3.8) TG608 (3.6) CT205 (6.3) CT176 (5.3) TG582 (6.5) A35.7 (18.9) A35.9 (0.0) TG484 (22.1) TG337 (36.2) CT59 (36.3) TG620 (0.9) TG250 (0.9) TG507 (1.5) EBR Chr3 TG114 (0.0) TG517 (2.2) TG132 (0.0) CT141 (21.3) CT22 (19.1) TG525 (2.3) A44 (8.5) TG66 (3.8) TG621 (4.9) S (3.5) CT82 (2.1) TG388 (1.4) TG515 (3.1) TG246 (6.0) XLRR.140 (8.4) TG411 (26.9) TG214 (13.1) Selective Genotyping 1.8 Chr4 TG483 (0.0) TG586 (8.0) PK PK (8.9) (2.6) CT157 (5.3) TG652 (3.8) TG65 (15.0) CT50 (13.7) CT73 (6.0) CT173 (5.4) CEL68 (4.3) TG163 (4.3) EBR5.2 EBR Chr5 CT101 (0.0) CEL5 (10.7) TG441 (13.1) CT242 (11.1) CT93 (23.9) PK (27.9) RLRR.220 (6.0) XLRR.370 (7.1) CT202 (2.0) TG318 (3.9) CT118 (2.0) CT172 (5.0) TG185 (14.9) 2.2 Chr6 CT285 (0.0) CT83 (13.6) TG232 (5.0) AN (4.7) TG590 (6.2) CT58 (6.6) CG43 (8.8) TG365 (10.2) TG253 (9.4) C54 (7.5) TG279 (8.5) CT107b (8.0) TG314 (20.7) 2.0 Chr7 TG499 (0.0) TG216 (17.6) CT226 (15.2) EBR8.1 TG183 (12.8) TG174 (4.0) PK (9.6) TG61 (10.1) CT135 (2.8) CT52 (11.2) C21 (31.9) TG128 (21.1) EBR Chr8 CD40 (0.0) TG176 (23.6) CT92 (14.7) TG349 (10.4) TG302 (6.4) TG330 (20.9) TG294 (22.4) CT68 (4.1) CT265 (25.0) EBR9.1 Chr9 CT143 (0.0) C11 (6.4) TG9 (1.6) TG254 (6.1) RLRR.140 (16.7) RLRR.130 (0.0) CLRR.950 (5.6) XLRR.360 (2.1) TG291 (12.5) TG551 (17.8) TG390 (7.1) S (5.6) TG248 (9.3) CT74 (8.1) TG421 (10.0) TG424 (5.6) TG429 (29.1) Chr10 TG230 (0.0) CT234 (7.7) TG566 (3.0) CT274 (0.7) CT287a (3.5) TG15 (7.0) CD34 (1.1) CC33 (10.4) KJB3 (0.0) CT57 (4.7) CEL79 (5.9) CEL58 (3.6) TG241 (6.3) TG403 (0.7) TG63 (16.4) EBR11.1 EBR11.2 Chr11 CT168 (0.0) TG508 (12.0) TG651 (5.8) TG523 (7.0) CT182 (9.2) TG147 (9.2) A41.3 (3.6) CT55 (3.6) CD17 (9.4) CT107a (5.7) TG546 (8.4) CT107c (3.7) TG36 (14.4) TG393 (26.7) EBR12.1 EBR12.2 EBR10.1 EBR Chr12 CT156 (0.0) TG111 (16.9) CT100 (12.3) TG68 (16.2) CT79 (3.8) CT211 (6.3) AN (11.1) TG180 (3.7) TG283 (0.7) TG565 (0.8) PK (10.4) TG473 (26.3) CT276 (8.1) KJB4 (14.4)
8 EB-R Breeding Lines Developed Fresh-Market Tomatoes»Cherry: Available»Grape: Available»Plum: Available»Med-Large Round: 1-2 years Processing Tomatoes: 1-2 years
9 Fresh Market Tomatoes Cherry Inbred Lines High Yield EB Resistant High Fruit Lycopene Determinate Semi-determinate Indeterminate
10 CHERRY Inbred Lines PSCH-2: Semi-determinate, limited EB, high yield, 3/4 inch fruit, high LYC, jtd PSCH-24: Semi-determinate, upright, limited EB, 1/2 inch fruit, high yield, good color, jtd PSCH-30: Semi-determinate, mid-size plant, very high yield, 3/4 inch fruit, good color, nice clusters, very healthy fruit, jtd PSCH-63: Indeterminate, high LYC, bit elongated fruit, 1- inch fruit, long clusters, EB resistance, jtd PSCH-66: Determinate, elongated fruit (1.5-inch), high LYC, very healthy fruit, high yield, jtd
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14 Fresh Market Tomatoes Grape Inbred Lines High Yield EB Resistant High Fruit Lycopene Semi-determinate Indeterminate
15 GRAPE Inbred Lines PSGR-23-1: Indeterminate, EB resistance, very high LYC, excellent clusters, good yield, very healthy fruit, sweet, jtl PSGR-27-1: Indeterminate, EB resistance, very high LYC, excellent clusters, high yield, very healthy fruit, jtl PSGR-30-1: Indeterminate, good resistance, very healthy fruit, nice fruit shape, very good fruit color, jtl PSGR-32-1: Indeterminate, good resistance, very healthy fruit and stem, large grapes, nice color, VERY SWEET, high yield, jtl PSGR-42-1: Indeterminate,disease resistance, very high LYC, VERY SWEET, very high yield, very nice fruit shape (elongated, cylindrical fruit), very healthy fruit, jtd (but very loose joint)
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20 Fresh Market Tomatoes Plums: Inbred Lines and Exper. Hybrids High Yield EB Resistant High Fruit Lycopene Determinate
21 PLUM Inbred Lines PSPL-1: Determinate, high LYC, thick walls, high yield, med size fruit, very firm, compact plant, healthy fruit, good combining ability, jtd PSPL-8-1: Determinate, fruit bit elongated (cylindrical), good color, good walls, extended ripening, fruit bit pointy, jtd (but loose joint) PSPL-8-3: Determinate, thick walls, very firm, very healthy fruit, elongated large fruit (cylindrical), fruit bit pointy, good color, jtd
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24 Fresh Market Tomatoes Medium and Large Round Tomatoes (Inbred lines available within 1-2 years) High Yield EB Resistant High Fruit Lycopene Determinate Semi-determinate
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28 Processing Tomatoes (Inbred lines available within 1-2 years) High Yield EB Resistant High Fruit Lycopene Determinate
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30 Late Blight (Phytophthora infestans)
31 Late Blight (Phytophthora infestans)
32 Genetic Resistance to LB in Tomato 3 known major resistance genes: Ph-1 Ph-1 (chr.. 7): confers resistance to race 0» Has been overcome by new races Ph-2 Ph-2 (chr.. 10): confers partial resistance to some isolates» Often fails in the presence of aggressive isolates Ph-3 Ph-3 (chr.. 9): Much stronger resistance» Some isolates have been identified that overcome Ph3
33 S. lycopersicum (NCEBR-2) X S. pimpinellifolium (PSLP153) LB Susceptible LB Resistant F 1 X F 2 X n = 1008 F 2 Plants LB Evaluation Genotyping Mapping F 3 Progeny Testing for LB Res.
34 Parents of the Mapping Population
35 Parents and F of 1 the Mapping Population NCEBR- 2 F 1 PSLP153 Resistance in PSLP153 is Completely Dominant
36 Mapping of a New LB Resistance Gene A NEW resistance gene (Ph-5) has been mapped to chr. 1 Ph-5 is mapped within a 10 cm region
37 Ph-5 Fine Mapping Developing NILs to fine map Ph-5 Ultimate goal is to clone Ph-5
38 Ph-5 NIL Development S. lycopersicum (NCEBR-2) X S. pimpinellifolium (PSLP153) F 1 X F 2 X F X 3 NCEBR-2 X NCEBR-2 X F 4 F 4 BC 1 NCEBR-2 X F 4 BC 2 Using a combination of MAS and PS F 4 BC 3
39 Late Blight Resistance Breeding!Lines developed (available Fall 2009): "Cherry Tomatoes: Ph-5 "Grape Tomatoes: Ph-5!Lines being developed (available 1-3 years): "Processing Tomatoes: Ph-5 "Large-size FM Tomatoes: Ph-5 "Processing Tomatoes: Ph-2 + Ph-3 "Large-size FM Tomatoes: Ph-2 + Ph-3!Lines plan to develop:
40 # Selected wild types: Lycopene! Tomato is a major source of lycopene " Other sources include watermelon, pink grapefruit, papaya, rosehip, cassava, apricot! Current tomato cultivars are low in Lycopene # Commercial cvs: µg/g
41 Known High-Lycopene Genes in Tomato hp1 (high pigment-1) hp2 Spontaneous mutations Both genes have serious undesirable pleiotropic effects Og c (old-gold crimson) A useful recessive gene (adding ~25% LYC) Not as high LYC as hp genes Low in beta-carotene
42 Search for New Sources of High Fruit Lycopene Screened ~300 wild accessions of tomato Identified a few exceptional accessions within S. pimpinellifolium Richest sources of lycopene in tomato Superior to hp1, hp2 and Og c NO known pleiotropic effects
43 Mapping QTLs for High Fruit Lycopene Content S. lycopersicum! S. pimpinellifolium F 1 X F 2 X F 3 X Mapped QTLs for Fruit Lycopene Content in F 2, F 3 and F 4 F 4
44 Development of RILs and Mapping QTLs for Lycopene Content S. lycopersicum! S. pimpinellifolium F 1 F 2 F 3 F 4 F 7 - RIL F 8, F 9, F 10 Mapped QTLs for Fruit Lycopene Content in F, F, F and F
45 Distribution of Fruit Lycopene Content in F 9 Generation 18 F Frequency S. lycopersicum S. pimpinellifolium Lycopene ug/g fresh weight
46 Two Stable Major QTLs for Fruit Lycopene Content -Markers closely linked with these QTLs -Fine mapping and NILs development
47 Marker-assisted Development of NILs for lyc7 and lyc12 One F 9 RIL selected for backcrossing QTLs were confirmed in BC 2 Lyc12 was determined very strong In heterozygous condition increases LYC by 70% compared with the homozygous recurrent parent 1500 NILs (BC 3 S 1 ) is being evaluated under field conditions to fine map the lyc12 interval
48 NIL Containing lyc12
49 High LYC Breeding Lines Developed Fresh-Market Tomatoes»Cherry: Available»Grape: Available»Plum: Available»Med-Large Round: 1-2 years Processing Tomatoes: 1-2 years
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57 High LYC Inbred Lines PSCH-2: Semi-determinate, limited EB, high yield, 3/4 inch fruit, high LYC, jtd PSCH-66: Determinate, elongated fruit (1.5-inch), high LYC, very healthy fruit, high yield, jtd PSGR-23-1: Indeterminate, EB resistance, high LYC, excellent clusters, good yield, very healthy fruit, sweet, jtl PSGR-27-1: Indeterminate, EB resistance, high LYC, excellent clusters, high yield, very healthy fruit, jtl PSGR-42-1: Indeterminate,disease resistance, high LYC, VERY SWEET, very high yield, very nice fruit shape (elongated, cylindrical fruit), very healthy fruit, jtd (but very loose joint) PSPL-1: Determinate, high LYC, thick walls, high yield, med size fruit, very firm, compact medium size plant, very healthy fruit, good combining ability, hybrids with
58 Acknowledgments Heather Merk Mathew Kinkade Hamid Ashrafi Funding: PDA, PVGA, MAFPA
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