Genetics and Genomics

A key element of our approach to studying the diversification in these fishes is the development of genomic resources to support the identification of genes underlying the phenotypic differences among species. We published the first linkage map for a cichlid (tilapia) in 1998, and have since developed an extensive set of markers, maps and large insert DNA clone libraries. These resources are described on our Cichlid Genome Resources www page and our new site BouillaBase.org.

Our genetic maps for East African species now include over 700 microsatellite markers, and we have developed physical maps based on the restriction fingerprints of more than 35,000 large-insert BAC clones. We have recently completed the sequencing and analysis of more than 116,000 ESTs from tilapia.


  • DiPalma F, Kidd C, Borowsky R, Kocher TD. Construction of bacterial artificial chromosome libraries for two model fish species: the Lake Malawi cichlid (Metriaclima zebra), and the blind cavefish (Astyanax mexicanus). 2007. Zebrafish 4: 41-47 (PDF)
  • Katagiri T, Kidd C. Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD. 2005. A BAC-based physical map of the Nile tilapia genome. BMC Genomics 6:89. (PDF)
  • Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, Hulata G, Slettan A, Stern JE, Terai Y, Kocher TD. 2005. A second generation genetic linkage map of tilapia (Oreochromis spp.) Genetics 170: 237-244. (PDF)
  • Carleton, KL, Streelman JT, Lee BY, Garnhart N, Kidd M, and Kocher TD. 2002. Rapid isolation of CA microsatellites from the tilapia genome. Animal Genetics 33(2):140-4. (PDF)
  • Streelman JT and Kocher TD. 2000. From phenotype to genotype. Evolution and Development 2:166-173. (PDF)
  • Kocher TD, Lee WJ, Sobolewska H, Penman D and McAndrew B. 1998. A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics 148:1225-1232. (PDF)




Labeotropheus trewavasae


Pseudotropheus tropheopsTropheops.jpg

Melanochromis auratusMelanochromis.jpg
Images by Justin Marshall