In the present study, we tested the congruence between the sdY sex-specific marker and other commonly used male markers, located on the Y-chromosome, with the sex phenotypes in 5 species of Pacific salmon in Asian waters, including Chinook, chum, sockeye, masu, and pink salmon. We found that the localization of the sex-specific marker of both males and females of these species is not consistent with the phenotypic sex. Also, no linkage was found between noncoding markers and the sdY gene in the same species samples. Possible genetic and physiological mechanisms underlying this discrepancy are discussed.

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