Tomato-Arabidopsis Synteny Map

The following links display the molecular marker linkage maps of the tomato genome. When you click on any chromosome, you will see two maps of each chromosome. The first map (left side of image) is the high density molecular marker map published by Tanksley et al. (1992). On the right is a new map (Fulton et al, in prep) based on COS markers. Connecting the two maps (dashed lines) are common markers on both maps. Because of the large number of markers on each chromosome, it will not be possible to read the individual marker names. To see an enlarged region of each chromosome, click on the individual BINS which will be highlighted at the right most part of the screen. This will take you to an enlarged map of that section of the chromosome in which the marker names will be readable. To link to the sequence for any marker, click on the corresponding marker name in the list to the right of the map.

Both maps (high density RFLP map and COS marker map) are based on F2 populations from the interspecific cross L. esculentum x L. pennellii. Details of the high density RLFP mapping population can be found in Tanksley et al. (1992). The COS marker map is based on 80 F2 individuals. Markers to the right of solid hash marks were ordered at a LOD > 3; markers next to dashed hash marks are ordered at a LOD > 2 but < 3; remaining markers are given in the most likely interval (< LOD 3). Markers next to a vertical bar cosegregate. The COS marker map development is part of an ongoing project for determining the syntenic relationship between the Arabidopsis and tomato genomes. The map will be updated periodically as new markers are added and new interactive features added for making syntenic comparisons. Potato and eggplant comparative maps will also be added soon.

If you have any questions regarding the maps, please email us at

Tanksley et al. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141-1160.