Characterization of DNA markers isolated from the gynogenetic triploid ginbuna ( Carassius auratus langsdorfi) by representational difference analysis

Abstract

Representational difference analysis (RDA) was carried out to isolate genetic markers for gynogenetic triploid ginbuna ( Carassius auratus langsdorfi) suitable for clarifying its genomic makeup. Four polymorphic DNA fragments were obtained by seven series of RDA, in which amplicons prepared from the diploid ginbuna or the goldfish ( C. a. auratus) as drivers were subtracted from those prepared from the triploid ginbuna as testers. These fragments detected presence- and absence-type in the amplicons prepared from C. auratus fishes. Hybridization analyses with each of these markers to genomic DNA revealed that these sequences were present in the DNA of all tested populations of C. auratus fishes, but were absent from the DNA of other cyprinid fishes. Thus, these markers could detect restriction fragment length polymorphisms among C. auratus fishes. Three out of four RDA markers were identified in the amplicons mainly from the triploid ginbuna and the goldfish. One remaining marker was shared between a clonal line of the triploid ginbuna and several individuals of the diploid ginbuna. These data provide additional evidence for the genomic contribution made by the ancestor(s) of the goldfish and the diploid ginbuna to the triploid hybrid ginbuna.