June 29, 2009 Tomato Genetics and Breeding at Penn State An Overview Majid R. Foolad
OUTLINE Traits of Interest Genetic and Breeding Research Breeding Activities Fresh-market breeding lines Processing breeding lines
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
Early Blight (Alternaria solani and A. tomatophila)
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
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
EB-R QTLs in different S. lycopersicum x S. habrochaites BC populations EBR1.1 7.0 2.4 Chr1 CT197 (0.0) TG24 (4.8) AN23.210 (4.5) AN23.230 (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) EBR2.1 4.4 Chr2 PK12.600 PK12.1200 (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) EBR3.1 2.9 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) S23.140 (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) PK34.150 PK34.300 (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 EBR5.1 3.7 Chr5 CT101 (0.0) CEL5 (10.7) TG441 (13.1) CT242 (11.1) CT93 (23.9) PK12.340 (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) AN23.410 (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) PK12.300 (9.6) TG61 (10.1) CT135 (2.8) CT52 (11.2) C21 (31.9) TG128 (21.1) EBR8.2 5.4 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) S11.210 (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 EBR9.2 8.2 6.8 3.8 5.3 Chr12 CT156 (0.0) TG111 (16.9) CT100 (12.3) TG68 (16.2) CT79 (3.8) CT211 (6.3) AN23.390 (11.1) TG180 (3.7) TG283 (0.7) TG565 (0.8) PK12.320 (10.4) TG473 (26.3) CT276 (8.1) KJB4 (14.4)
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
Fresh Market Tomatoes Cherry Inbred Lines High Yield EB Resistant High Fruit Lycopene Determinate Semi-determinate Indeterminate
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
Fresh Market Tomatoes Grape Inbred Lines High Yield EB Resistant High Fruit Lycopene Semi-determinate Indeterminate
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)
Fresh Market Tomatoes Plums: Inbred Lines and Exper. Hybrids High Yield EB Resistant High Fruit Lycopene Determinate
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
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
Processing Tomatoes (Inbred lines available within 1-2 years) High Yield EB Resistant High Fruit Lycopene Determinate
Late Blight (Phytophthora infestans)
Late Blight (Phytophthora infestans)
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
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.
Parents of the Mapping Population
Parents and F of 1 the Mapping Population NCEBR- 2 F 1 PSLP153 Resistance in PSLP153 is Completely Dominant
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
Ph-5 Fine Mapping Developing NILs to fine map Ph-5 Ultimate goal is to clone Ph-5
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
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:
# Selected wild types: 200-250 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: 50-75 µg/g
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
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
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
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
Distribution of Fruit Lycopene Content in F 9 Generation 18 F 1 16 14 Frequency 12 10 8 6 S. lycopersicum S. pimpinellifolium 4 2 0 0 20 40 60 80 100 120 140 160 180 200 Lycopene ug/g fresh weight
Two Stable Major QTLs for Fruit Lycopene Content -Markers closely linked with these QTLs -Fine mapping and NILs development
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
NIL Containing lyc12
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
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
Acknowledgments Heather Merk Mathew Kinkade Hamid Ashrafi Funding: PDA, PVGA, MAFPA