The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Fig 5
Sockeye salmon and kokanee sex chromosomes.
A) A GWA between all known male and female sockeye salmon and kokanee salmon with the DAPC LD1 values as covariates. The two peaks (Chr. 9a and 9b) did not reach significance. B) A GWA between all individuals scored for the presence or absence of the sex-determining gene (red line indicates significance threshold). C) A depiction of the proposed X1 (9b), X2 (9a), and Y chromosomes. D) IGV was used to visualize variants on chromosome 9a with only minimal filtering for known females (no upper Columbia River kokanee), males (no upper Columbia River kokanee), Freshwater Fisheries Society of British Columbia female kokanee, and Freshwater Fisheries Society of British Columbia male kokanee. E) On the left, LD plot of chromosome 9a from 4.6 Mbp to the end of the chromosome (~2 Mbp) with a minimum LD threshold of r2 = 0.5 for both plots. On the right, LD plot of chromosome 9b from 3.5 Mbp to 11.5 Mbp.