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

Abstract

Whole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e. heterochiasmy), 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. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. 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.

Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

“…Although the functional annotation for these two genes in American lobster is unknown, future work may provide information on the sex determi- Palti et al, 2015;Sutherland et al, 2016). For further discussion of these consistencies across the salmonid phylogeny in terms of sex chromosomes, see Sutherland, Rico, Audet, and Bernatchez (2017).…”

Sex-specific co-expression networks and sex-biased gene expression in the salmonid Brook Charr Salvelinus fontinalis

“…Brook Charr used in this study were originally used to construct a low-density genetic map for reproductive (Sauvage, Vagner, Derôme, Audet, and Bernatchez 2012a), growth and stress response QTL analyses (Sauvage, Vagner, Derôme, Audet, and Bernatchez 2012b). They were used to construct a high-density genetic map that was integrated with the other salmonids (Sutherland et al 2016), then used to identify QTL, sex-specific recombination rates, and the Brook Charr sex chromosome (Sutherland et al 2017). The 192 F 2 individuals were full sibs from a single family resulting from a cross of an F 1 female and F 1 male that were from an F 0 female from a wild anadromous population (Laval River, near Forestville, Québec) and an F 0 male from a domestic population (Québec aquaculture over 100 years).…”

“…F 2 offspring were raised until 65-80 g and then 21 phenotypes were collected along with several repeat measurements to determine growth rate. Full details on these phenotypes are previously described (Sauvage et al 2012a, 2012b), including sex-specific phenotype averages, standard deviations, and phenotype correlations for all 192 offspring (see Table S1 and Figure S2 from Sutherland et al 2017). The 15 phenotypes used in the present study to correlate with co-expression modules were maturity, length, weight, growth rate, condition factor, liver weight, post-stress cortisol, osmolality and chloride, change in cortisol, osmolality and chloride between one week before and three hours after an acute handling stress, egg diameter, sperm concentration, and sperm diameter.…”

Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout

“…Linkage maps have been used to map loci associated with disease resistance (Houston et al 2008;Moen et al 2009), life history and physiological trait variation (Rogers et al 2007;Miller et al 2012; Gagnaire et al 2013a;Sutherland et al 2017;Pearse et al 2019), and commercially valuable traits (Gonzalez-Pena et al 2016) in salmonids and have been instrumental in the assembly of salmonid reference genomes (Lien et al 2016, Christensen et al 2018a, 2018bPearse et al 2019;Sävilammi et al 2019). A linkage map for lake trout would enable the application of cutting-edge genomic tools to questions in lake trout management and evolution and would aid in the identification of loci underlying phenotypic variation and local adaptation.…”