Several genetic linkage maps of cichlid fishes have been constructed. Our latest map, based on an interspecific F2 cross between O. niloticus and O. aureus has an average spacing of 3cM between microsatellite markers (Lee et al. 2005 - PDF.
We have also published a map for Lake Malawi cichlids, based on the F2 of an intergeneric cross of two Lake Malawi cichlids (Metriaclima zebra and Labeotropheus fuelleborni). Although this map has fewer markers, we were able to select markers from the tilapia map to fill in gaps. When we compare marker orders in these two maps, we find only two obvious rearrangements, indicating that gene order is largely conserved across this group of fishes.
| Species | Family type | # markers | marker type | Institution | Reference |
| Tilapia | F2 | 550 | microsatellite | HCGS | Lee et al., 2005 |
| Malawi | F2 | 137 | microsatellite | HCGS | Albertson et al., 2003 |
| Tilapia | F2 | 229 | micro/AFLP | UC Davis | Agresti et al., 2000 |
| Tilapia | BC | 37 | microsatellite | Univ Wales | McConnell et al., 2000 |
| Tilapia | haploid | 162 | micro/AFLP | HCGS | Kocher et al., 1998 |
Four tilapia BAC libraries have been produced at the Tokyo University of Fisheries (Katagiri et al. 2000) (PDF). Plates and filters for portions of libraries 3 and 4 are available. Contact Tom Kocher for more information.
| Library | # primary clones | Average insert size | Estimated coverage | Picked |
| 1 | 120k | 65k | 6x | - |
| 2 | 800k | 105k | 65x | - |
| 3 | 100k | 145k | 11x | 36k |
| 4 | 40k | 194k | 6x | 33k |
A BAC library has been constructed for the Lake Malawi cichlid Metriaclima zebra by DiPalma et al. (2007) [PDF]. This library is also available at cost by contacting Tom Kocher (tdk@umd.edu).
A library from the Lake Victoria cichlid Haplochromis chilotes (10x coverage, 128kb average insert size) has been constructed at the Tokyo Institute of Technology by Watanabe et al. (2003). [PDF]
A third haplochromine library, from the Lake Tanganyika species Astatotilapia burtoni (12x coverage, 150kb average insert size), has been constructed by Michael Lang in Chris Amemiya's lab, in a collaboration with Axel Meyer at the University of Konstanz (Lang et al., 2006). (PDF)
With support from the US Dept. of Agriculture, we have fingerprinted more than 35,000 clones from tilapia libraries 3 and 4 (approximately 5x coverage of the genome) and produced a physical map of overlapping BAC clones Katagiri et al. (2005) [PDF]. An FPC file of the fingerprint data is available from Tom Kocher (tdk@umd.edu).
There are many labs around the world working to develop cDNA resources for cichlids. Hans Hofmann (Univ Texas, Austin) is organizing a cichlid microarray collaboration.
| Laboratory | Species | Tissue | # ESTs | Online |
| Okada | Paralabidochromis chilotes | jaw | 20,701 | Gene Index |
| Okada | Ptyochromis 'redtail sheller' | jaw | 13,752 | Gene Index |
| Okada | Lipochromis 'matumbi hunter' | jaw | in progress | |
| Fernald/Hofmann/Meyer | Astatotilapia burtoni | several | 10,212 | Gene Index |
| Meyer | Metriaclima zebra | skin | in progress | |
| Nagahama | Oreochromis niloticus | developing gonad | 18,186 | NIBB |
| Kocher | Oreochromis niloticus | various | 116,899 | BouillaBase |
| Baroiller/D'Cotta | Oreochromis niloticus | brain and gonad | in progress | |
| Jaso-Friedman | Oreochromis niloticus | nonspec. cytotoxic cells | in progress | |
| Genomar asa | Oreochromis niloticus | brain/gill | 2,500 | |
| Martins | Oreochromis niloticus | brain/heart/muscle | in progress | |
| Total | >182,000 |
| University of Maryland, College Park |  |