Genome‐wide association analyses based on whole‐genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes

Abstract Identification of sex determination system and sex‐determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius , were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex‐determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes ( F ST ranged from 0.245 to 0.556). Of the 150 sex‐associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex‐specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex‐associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius . More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that “Z dosage” effect might play a vital role in the processes of sex determination/differentiation. These sex‐specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.