Markers for Tomato Chromosome 6

See SGN site for chromosome map


Updated, 4 May 2009



Marker cM PCR primers Marker sequence Sequence for tomato genotypes Comments
CT216 0.0 CT216F2-R2 See SGN Yes (PDF) Gh25=Gh13=GMp6330=Heinz=PR
LE_HBa0107A05 3.0 CM1F1/R1 See SGN Yes (PDF) HUJ-VF=Gc9=Gc143
LE_HBa0246L12 3.0 CM2F1/R1 See SGN Yes (PDF) HUJ-VF=Gc9=Gc143-2, Gc43 differed by 11 SNP and 2 INDEL
TO270 3.0 TO270F1/R2 See SGN Yes (PDF) Heinz = Gc2711=GMp6330 not equal GMh8632
At1g07080 3.5 cos II, see SGN     Heinz = Gc2711 not equal GMh8632
LE_HBa0118F10 5.0 CM7-F1/R1 See SGN Yes (PDF) Gc9=Gc43=Gc143-2, Heinz 1706 differed by 30 SNP
LE_HBa0037I09 5.0 CM5-F1/R1 See SGN Yes (PDF) Gc143-2=Gc9=HUJ-VF=Heinz 1706, Gc43 differed significantly
LE_HBa0185J10 5.0 CM6-F1/R1 See SGN Yes (PDF) Gc143-2=Gc43=Gc9, HUJ-VF Differs by 2 SNP
Mi23 5.5 Mi23F/Mi23R contact Maxwell Mi23-locus (pdf) co-dominant SCAR marker for Mi-1.2 gene
Mi locus 5.5 PM3F/PM3R contact Maxwell AY731232 matches BAC: HBa0112G05
Mi 1.2 5.5 PM3Fb/PM3Rb YES   Two-step PCR for detection of Mi1.2
Mi 1.2 5.5 PMiF3/PMiR3 YES YES different PCR patterns for genotypes
LE_HBa0250I21 5.5 CM4F1/CM4R1 See SGN Yes (PDF) Gc143-2=Gc9=Gc43, HUJ-VF differs by 7 SNP
LE_HBa0019E05 5.5 P6-6-F1/R1 See SGN YES (PDF) Gc9=Gc43, HUJ-VF differs significantly
REX ca.5 REXF1/R2 YES YES, tags Ty-1 (two TaqI sites) sequence for species (pdf, chapter I)
SSR48 6.0   see SGN NO, smear with PCR  
At5g61510 6.2 DM6-F2/R2 COS II, see SGN NO multiple PCR bands with Heinz
SSR47 6.5   see SGN NO, smear with PCR  
SSR128     see SGN NO PCR fragments  
LE_HBa0215K10 9.0 CM8-F1/R1 see SGN Yes (PDF) Gc43=Gc9, Heinz 1706 differed by 17 SNP
TG178 10.0 TG178F5/R5 see pdf file Yes (pdf file) Heinz different than GMh8632 =GIh902a=GMp6330
At3g10920 13.0 DM6-F4/R4 see SGN Yes (pdf file) PR=Gh13=Heinz, not equal Gh8632 = Gc9 , not equal LA1777
T0774 18.0 T0774F2/R2 See SGN Yes (pdf file)

Gh25=GMh8632=Gc2711= Gc43 (68a) .

Mandarina = PR≠Gh25 (10 SNP)

T0774 18.0 T0774F2/R2 See SGN Yes (pdf file) Gc171 = Purple Russian, not equal to LA1932 or Gh25-6
At3g56040 19.0 P6-19F1/R1   Yes (pdf file) Introgression for Ty-3
TG590 22.00 TG590F2/R2 See SGN Yes (pdf file) Heinz differed significantly from the breeding lines. Gh13 most closely matched with the two species.
  24.0 P6-24CF1/CR! AY248742   co-dominant SCAR marker for Ty-3 introgression
FLUW-25 25.0 FLUW25F/R   Yes (pdf file) PCR based tag for Ty-3 locus
G8 Locus 25.0 G8F3/R3 AY678298 Yes (PDF)

(Ty3 locus)

PR = BAC Clone, not equal Gc171 not equal GMh8632

G10 25.0 Uof FL AY678298 Yes (PDF) BAC sequence not equal Gh13 not equal Gc171, Ty-3 locus
FER 25.0 P6-25F2/R5 AY678298 (BAC) Yes (pdf) co-dominant SCAR marker for Ty-3, Ty3-a, and Ty-3b introgressions
T0507 25.00




Yes (F2/R2 pdf file)

Yes (F2/R1 pdf file)

Gc9=Gh13, species are similar, Heinz differs significantly
At4g27700 27.0 COS II See SGN YES Tag TyA (Ty3) gene for GV resistance
HBa0167M06 28.0 p6-28 F1/R2 See S Yes (pdf file)  
T1098 30.00 COS See SGN Yes (PDF) 19a=35a=88a=100a=113a=W28=Gh13. Mandarina=68a=Purple Russian. The two groups differ by 8 SNP.
TG118 ca. 30 SLm0047K24 Peters et al. 2009    
T0834 32.0 HBa0307J13 Peters et a. 2009 YES (PDF) Introgression for Ty3
T0834 32.00 COS See SGN Yes (PDF) Heinz=PR, 100a=19a=35a=228-2=Gh13, 38 SNP and 8 INDEL between the resistant and susceptible lines.
TG352 33.5 TG352F2/R1 See SGN Yes (pdf file) Purple Russian=Mandarina=19a= 100a=68a=113a
At1g44835 38.3 P6-38.3 See SGN YES (pdf file) Introgresssion for BW resistance
At1g03150 41 P6-41F4/R4 See SGN YES (pdf file) Introgression for BW resistance
TG73 43.3 CMTG73F1/R2 See SGN YES (PDF file) HUJ-VF=Gc171
TG472 44.0 TG472F2/R2 See SGN Yes (pdf file) 19a=88a=68a=100a=228-2= Gh13=Heinz=Mandarina=Purple Russian=Cerasiforme=113a=Gc9
TG365 50.0 TG365F2/R2 See SGN YES (pdf file) Heinz=Gh13=Gc9, LA1777 differs significantly
TG253 55.0 CMTG253F1/R1 See SGN YES (pdf file) HUJ-VF=Gc171
TG292 64.0 YES See SGN YES (pdf file) Heinz=Gc171=Gh13, differs from LA1777 by 22 SNP
TG579 73.0 TG579F1/R1 See SGN YES (pdf file) Heinz=Gh13=Gc9, LA2779 differs by 15 SNP
CT90 76.0 CMCT90F1/R2 See SGN YES (PDF file) HUJ-VF=Gc171
TG279 80.0 TG279F2/R1 See SGN YES (pdf file) Heinz=Gh13=Gc9, LA1777 differs by 10 SNP and one INDEL
LE_HBa0169D11 85.0 CMTy4AF2/R1 See SGN YES (pdf file) Cera=Gc171=HUJ-VF
SL_MboI0011K15 92.7 CMTy4CF1/R1 See SGN YES (pdf file) Cera=Gc171=HUJ-VF
LE_HBa0217M17 97.0 CMTy4BF1/R2 See SGN YES (pdf file) HUJ-VF=Gc171=Cera
TG221 101.0 CMTG221F2/R1 See SGN YES (pdf file) HUJ-VF=Gc171




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