Supplemental Material for Smith et al., 2020

Document S1: Detailed description of library preparation, RNA bait design, and targeted sequence capture methods.

Document S2: Map information, phenotypes, and genotypes used for QTL and sex locus mapping.

Table S1: The lake trout linkage map and sequences of mapped RAD loci.

Table S2: Centromere mapping intervals for each linkage group

Table S3: Candidate genes identified for significant QTL peaks.

Table S4: Estimated recombination rates for each linkage group

Figure S1: Alignments of lake trout linkage groups with Arctic char chromosomes.

Figure S2: Alignments of lake trout linkage groups with rainbow trout chromosomes.

Figure S3: Alignments of lake trout linkage groups with Atlantic salmon chromosomes.

Figure S4: Dot plot grid comparing the lake trout linkage map with the Arctic char genome assembly.

Figure S5: Dot plot grid comparing the lake trout linkage map with the rainbow trout genome assembly.

Figure S6: Dot plot grid comparing the lake trout linkage map with the Atlantic salmon genome assembly.

Figure S7: MapComp dot plot grid comparing the lake trout linkage map with the brook trout linkage map from Sutherland et al. (2016).

Figure S8: Centromere mapping using half tetrad analysis.

Figure S9: Boxplots of recombination rate estimated for each linkage group for males and females.