Representational difference analysis, high-resolution physical mapping, and transcript identification of the zebrafish genomic region for a motor behavior

Abstract

Zebrafish is one of the best model organisms for investigating gene functions in vertebrates. By 4,5′,8-trimethylpsoralen mutagenesis, we isolated a zebrafish mutant, vibrato, with defects in the spontaneous contraction and touch response. Whole genome subtraction between the wild-type and the mutant genomes by representational difference analysis yielded polymorphic markers tightly linked to the vibrato locus. Using these markers, we constructed a high-resolution physical map and localized the vibrato locus within a genomic region of 720 kb. Direct cDNA selection with the contig led to the identification of a novel gene, solo, encoding a protein with SEC14 and spectrin repeat domains. These domains of Solo shared significant amino acid sequence identities with those of mammalian Trio and Karilin. In addition, we found the zebrafish orthologs for mammalian TTN, COL5A2, and CED-6 in the vibrato region. Mapping of these genes localized human chromosomal regions possibly involved in motor disorders. Our results suggest that representational difference analysis provides an efficient way to isolate mutated genomic regions in zebrafish.