Genome Sequencing of 20 Tasmanian Atlantic Salmon Used to Characterize Multiple Loci Associated with Sex Determination

Farmed Atlantic salmon is globally important, including in Australia where selective breeding has been in progress since 2004. To explore aspects of population diversity and evolution, we selected 20 animals from the Tasmanian breeding population for whole genome sequencing. This generated 38X average mapped coverage per fish using Illumina short read technology, before variants were called against reference genome assembly ICSASG_v2. A total of 13.6 M variants were identified after quality filtering, comprising 10.1 M SNP and 3.5 M indels. Patterns of SNP variation allowed unbiased comparisons to be made against European and North American derived salmon genomes, and PCA of genetic distance was performed to reveal significant splits between populations. A particular focus was applied to genomic regions likely to direct sex determination. We performed SNP chip based GWAS using 2889 animals to confirm an earlier report describing the presence of at least 3 distinct loci controlling sex determination. To characterize these genomic regions, raw reads were mapped against an available sdY BAC contig generated from a male fish. Analysis of read depth and SNP heterozygosity in male and females revealed the precise breakpoints bounding the male specific region. We then compared sdY region SNP haplotypes between males, and found divergence corresponding to sex lineage membership. We have used these findings to draw conclusions about the likely evolutionary pathway that has generated multiple sex lineages in Tasmanian Atlantic salmon.