A radiation hybrid map of the zebrafish genome

Recent large-scale mutagenesis screens have made the zebrafish the first ve rtebrate organism to allow a forward genetic approach to the discovery of d evelopmental control genes(1-3). Mutations can be cloned positionally, or p laced on a simple sequence length polymorphism (SSLP) map(4-6) to match the m with mapped candidate genes and expressed sequence tags(7,8) (ESTs). To f acilitate the mapping of candidate genes and to increase the density of mar kers available for positional cloning, we have created a radiation hybrid ( RH) map of the zebrafish genome. This technique is based on somatic cell hy brid lines produced by fusion of lethally irradiated cells of the species o f interest with a rodent cell line. Random fragments of the donor chromosom es are integrated into recipient chromosomes or retained as separate minich romosomesg (9,10) The radiation-induced breakpoints can be used for mapping in a manner analogous to genetic mapping, but at higher resolution and wit hout a need for polymorphism. Genome-wide maps exist for the human, based o n three RH panels of different resolutions(11-13), as well as for the dog(1 4) rat(15) and mouse(16, 17). For our map of the zebrafish genome, we used an existing RH panel (18, 19) and 1,451 sequence tagged site (STS) markers, including SSLPs, cloned candidate genes and ESTs. Of these, 1,275 (87.9%) have significant linkage to at least one other marker. The fraction of ESTs with significant linkage, which can be used as an estimate of map coverage , is 87.9%. We found the average marker retention frequency to be 18.4%. On e cR(3000) is equivalent to 61 kb, resulting in a potential resolution of a pproximately 350 kb.