Markers for Tomato Chromosome 6
See SGN site for chromosome map
(www.sgn.cornell.edu)
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 | T0507F2/R2 T0507F2/R1 |
No | 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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