Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook Charr Salvelinus fontinalis

Abstract

Whole genome duplication can have large impacts on genome evolution. However, much remains unknown about these impacts, such as the mechanisms of coping with a duplicated sex determination system, which may result in increased sex determination mechanism diversity. Sexual conflict (i.e. alleles having different optimums in each sex) can result in sequestration of genes into non-recombining sex chromosomes. Development of sex chromosomes may involve heterochiasmy (i.e. sex-specific recombination rate), which is also poorly understood. Family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have non-homologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook Charr Salvelinus fontinalis and compare sex chromosome identities across the lineage (eight species, four genera). Although non-homology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify QTL for 21 unique growth, reproductive and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.