A Sex-Determining Gene (sdY) Assay Shows Discordance between Phenotypic and Genotypic Sex in Wild Populations of Chinook Salmon

Sex is determined genetically in most fishes, but the gene responsible for sex determination is not known for the vast majority of fish species, including Chinook Salmon Oncorhynchus tshawytscha. The purpose of this study was to characterize a putative sex-determining gene (sexually dimorphic on the Y-chromosome [sdY] gene) in Chinook Salmon and develop a method to test genomic DNA (gDNA) samples for genetic sex assignment. Using next-generation sequencing and salmonid DNA sequence data from GenBank, the entire genomic organization of Chinook Salmon sdY was described. The corresponding full-length complementary DNA (cDNA) sequence generated from total RNA was determined by using a combination of genomic-based primers and rapid amplification of cDNA ends (RACE) PCR assays. A phylogenic analysis was conducted by comparing the Chinook Salmon sdY cDNA sequence with sdY sequences (GenBank) from 10 other teleost species. A multisequence alignment was performed, and a phylogenetic tree was inferred from the alignment, providing evidence for sdY identity. Based upon a TaqMan real-time PCR assay, a genetic test for male sex using sdY was developed and tested on gDNA isolated from phenotypic female and male Chinook Salmon representing populations in Alaska, Idaho, and Washington. The results provide compelling evidence that sdY is the sex-determining gene in Chinook Salmon. We developed a reliable assay for sdY that can be used for genetic sex assignment in this species. However, discordance between phenotype and genotype was noted in 13 of 107 phenotypic female Chinook Salmon from Alaska and Washington. Several explanations for this discordance are discussed.