Isolation of a sex chromosome-specific DNA sequence in the medaka, Oryzias latipes

In the medaka, Oryzias latipes, which does not have cytologically recognizable sex chromosomes, the mechanism of sex determination (XX/XY) can be revealed by genetic crosses using a particular pigment gene. Since the only known sex-linked marker is this pigment gene, little information is available on the genetic maps of the medaka's sex chromosomes. High resolution genetic maps of its sex chromosomes are necessary to hunt for the sex-determining factor by the positional cloning method. In the present study, we isolated a sex-linked marker using the genomic differences between inbred strains of medaka. We established a congenic strain whose sex-determining region is derived from the HNI strain and whose genetic background is derived from the Hd-rR strain. Using differences between the genomes of the congenic and Hd-rR strains, we isolated a sex-linked clone (pHO5.5) from a random genomic library constructed from the HO5 strain of medaka. The pHO5.5-related sequences were conserved among Oryzias species. A linkage analysis using backcross progeny from the Hd-rR and HNI strains demonstrated perfect linkage between the pHO5.5-related sequence and the sex. We, hence, designated the locus of the pHO5.5-related sequence on sex chromosomes of medaka as Sex-Linked 1 (SL1). Using this sequence, we could identify the sex of inbred strains of medaka by PCR or Southern blotting. This sequence may be useful for genetic mapping on the sex chromosomes. We also discuss the availability of the congenic strain established in this study for isolating other sex-linked clones.