Mapping and evolution of candidate sex determining loci, sex chromosomes, and sex linked sequences in rainbow and cutthroat trout

Fish provide an intriguing model for the study of how sex determination mechanisms evolve. Salmonids have an XX-XY mechanism for sex determination where males are the heterogametic sex. Sex chromosomes of most salmonid species can not be cytogenetically distinguished suggesting that they are at an early stage of evolution. Salmonids have also evolved from a common tetraploid ancestor 25-100 million years ago. The role of genome duplications in shaping the karyotype of vertebrates is well established. The presence of a genome duplication event in salmonids' recent evolutionary history makes them a good model for understanding the structuring of genomes following polyploidization. This dissertation examines the evolution of sex determination mechanisms, and the evolution of duplicated loci following polyploidization using the two model salmonid species rainbow trout (Oncorhynchus mykiss ) and cutthroat trout (Oncorhynchus clarki). In this dissertation, we first show that unlike other Pacific salmon and trout species examined, rainbow and cutthroat trout have their sex locus on the same linkage group which appears to be largely homologous. We then use a BAC clone containing sequences of one of the markers used to establish synteny between the sex chromosomes of the two species, to identify the Y chromosome of cutthroat trout. We also test the linkage of a number of candidate sex-determining genes to the Y chromosome of rainbow trout. We exclude the role of all of the tested genes as candidates for sex-determination. We also describe duplication of one of the candidate genes, Sox6 and discuss its inheritance in our mapping families. Sox9, a candidate sex-determining gene is part of a chromosomal block shown to be conserved among different species. Recent evidence indicates conservation of the block in rainbow trout. Two Sox9 gene copies were isolated from rainbow trout, Sox9 and Sox9alpha2. Previous evaluations of their evolutionary history gave ambiguous results. We hypothesize that mapping of Sox9 and Sox9alpha2 would allow us to more properly evaluate their evolutionary relationship. The map position of Sox9 and Sox9alpha2 genes indicates that Sox9 belongs to the Sox9b clade while Sox9alpha2 belongs to the Sox9alpha clade.