GENE-MAPPING IN ZEBRAFISH USING SINGLE-STRAND CONFORMATION POLYMORPHISM ANALYSIS

To exploit fully the power of the zebrafish system as a model for vert ebrate development, it will be necessary to develop efficient tools fo r genomic analysis. In this report we have tested whether single-stran d conformation polymorphism analysis (SSCP) can be utilized for gene m apping in zebrafish. Over 100 primer pairs derived from noncoding regi ons of known genes and partially characterized cDNAs were analyzed, an d a polymorphism frequency of approximately 50% was detected in zebraf ish strains used for genetic mapping studies. A subset of these polymo rphic cDNAs was localized on the zebrafish map. SSCP thus represents a n efficient strategy for mapping transcribed sequences with a high res olution in the zebrafish genome, which will facilitate the integration of existing zebrafish framework maps, the generation of a zebrafish E ST map, and the application of alternative gene localization strategie s such as comparative mapping. (C) 1998 Academic Press.