The Organization of the Atlantic Salmon (Salmo salar) sdYGene and its Potential Genomic Environments

In the family Salmonidae males are the heterogametic sex, and SEX refers to the male phenotype. Salmonids lack morphologically distinct X and Y chromosomes; rather, a SEX locus or gene is considered to regulate sex-determination. Sex associated linkage markers are not consistent between salmonid species, leading to two competing sex-determining gene hypotheses. One hypothesis is that salmonids all share a common sex-determining gene. The alternative hypothesis is that different groups of salmonids have different sex-determining genes. Recently the sex-determining gene in rainbow trout (Oncorhynchus mykiss) was identified as sdY, a paralog of Interferon regulatory factor 9 (Irf9). Bacterial artificial chromosome (BAC) clones containing sdY were identified, isolated, shotgun sequenced, and assembled from the CHORI-214 BAC library (which came from a male Atlantic salmon). The aim of this project is to characterize the sex-determining region in order to understand the mechanism by which sdY can move from location to location. By comparing the region of sdY and its surrounding male sequence with the female equivalent region, the male specific genomic insertion point may be revealed. The search for the borders of male specific and female/male specific sequence reveals highly repetitive regions. They may contain informative sequence elements such as retrotransposons and transposable elements that could explain how the sdY gene moves from location to location in the genome.