RENN, Suzy C.P.; AUBIN-HORTH, Nadia; ANNIS, Sarah W.; HOFMANN, Hans A; Bauer Center for Genomics Research, Harvard University: Comparative Functional Genomics and the Study of Complex Phenotypes In “Non-Model” Organisms

The recent and rapid speciation of African Cichlids has produced a wealth of behavioral and morphological phenotypes with little genomic divergence and thus offers an excellent system for comparative functional genomics of complex traits. To date, most microarrays have been developed for relatively few model species whose genomes have been sequenced. However, as genomics matures into a comparative research program, it is becoming clear that expression profiling provides a powerful tool for non-model systems as well. Here we present a microarray constructed with ~5000 ESTs, representing ~3500 genes, derived from a brain cDNA library constructed from the African cichlid fish Astatotilapia (Haplochromis) burtoni. We extensively tested this array using both DNA and RNA from eight fish species in order to demonstrate the validity of cross-species hybridizations, thus expanding the possibilities of comparative functional genomics. We present an integrated approach to study the effect of genetic variation on gene expression profiles that underlie complex phenotypes. The array results are most robust when sample RNA is derived from closely related cichlids, furthermore we demonstrate consistent hybridization for closely related families (e.g., guppies and swordtails) and even very distantly related species (e.g., salmon and zebrafish). This microarray is a first step to bring genomics to bear in cichlids and other non-traditional model systems.