Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus).

We have generated a high-density, high-throughput genotyping array for characterizing genome-wide variation in Arctic charr (Salvelinus alpinus). Novel single nucleotide polymorphisms (SNPs) were identified in charr from the Fraser, Nauyuk and Tree River aquaculture strains, which originated from northern Canada and fish from Iceland using high coverage sequencing, reduced representation sequencing and RNA-seq datasets. The array was designed to capture genome-wide variation from a diverse suite of Arctic charr populations. Cross validation of SNPs from various sources and comparison with previously published Arctic charr SNP data provided a set of candidate SNPs that generalize across populations. Further candidate SNPs were identified based on minor allele frequency, association with RNA transcripts, even spacing across intergenic regions and association with the sex determining (sdY) gene. The performance of the 86,503 SNP array was assessed by genotyping Fraser, Nauyuk and Tree River strain individuals, as well as wild Icelandic Arctic charr. Overall, 63,060 of the SNPs were polymorphic within at least one group and 36.8% were unique to one of the four groups, suggesting that the array design allows for characterization of both within and across population genetic diversity. The concordance between sdY markers and known phenotypic sex indicated that the array can accurately determine the sex of individuals based on genotype alone. The Salp87k genotyping array provides researchers and breeders the opportunity to analyze genetic variation in Arctic charr at a more detailed level than previously possible.

A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication.

Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.

Hidden genetic variation evolves with ecological specialization: the genetic basis of phenotypic plasticity in Arctic charr ecomorphs.

The genetic variance that determines phenotypic variation can change across environments through developmental plasticity and in turn play a strong role in evolution. Induced changes in genotype-phenotype relationships should strongly influence adaptation by exposing different sets of heritable variation to selection under some conditions, while also hiding variation. Therefore, the heritable variation exposed or hidden from selection is likely to differ among habitats. We used ecomorphs from two divergent populations of Arctic charr (Salvelinus alpinus) to test the prediction that genotype-phenotype relationships would change in relation to environment. If present over several generations this should lead to divergence in genotype-phenotype relationships under common conditions, and to changes in the amount and type of hidden genetic variance that can evolve. We performed a common garden experiment whereby two ecomorphs from each of two Icelandic lakes were reared under conditions that mimicked benthic and limnetic prey to induce responses in craniofacial traits. Using microsatellite based genetic maps, we subsequently detected QTL related to these craniofacial traits. We found substantial changes in the number and type of QTL between diet treatments and evidence that novel diet treatments can in some cases provide a higher number of QTL. These findings suggest that selection on phenotypic variation, which is both genetically and environmentally determined, has shaped the genetic architecture of adaptive divergence in Arctic charr. However, while adaptive changes are occurring in the genome there also appears to be an accumulation of hidden genetic variation for loci not expressed in the contemporary environment.