Identification of the sex determination region and the development of a marker to distinguish males and females in megai abalone (Haliotis gigantea)

Sex identification markers are of considerable value to aquaculture and fisheries as they enable pre-maturity prediction of the genotypic sex of individuals as well as of the sex ratio in offspring. For these reasons, extensive investigations of the mechanisms of sex determination have been conducted in commercially important finfish species, resulting in the development of sex identification markers for many of these. However, research on shellfish is still in its infancy stage. In this study, we investigated the genomic basis of sex determination in megai abalone ( Haliotis gigantea ), a gastropod species of economic importance in fisheries and aquaculture in East Asia, with the aim of developing a sex identification marker. Initially, we examined the applicability of sex identification markers reported for two other Haliotis species, but found they were not transferable to H. gigantea. We then analyzed the sex chromosomes in H. gigantea using a whole-genome resequencing approach. By calculating the fixation index value between 10 females and 10 males, we identified a genomic region spanning approximately 2 Mb that exhibited nucleotide sequence divergence between the sexes on chromosome 18. This region was located next to the pseudoautosomal region which is characterized by an absence of sequence differentiation between the sexes. In the divergent region, male-specific SNPs were identified but no female-specific SNPs were detected, indicating that this species has an XX-XY sex determination system. By exploring Indel polymorphisms in the divergent region, we successfully developed a codominant PCR marker for sex identification that could be applied to wild individuals from geographically distant locations. A cross-species analysis suggested that the sex determination region in H. gigantea was unlikely to be shared with the closely related species H. discus hannai . This raises the possibility of a widespread, rapid turnover of sex chromosomes or sex determination regions in abalones, similar to certain vertebrate lineages such as finfish. • The sex-determining region in Haliotis gigantea was identified. • A codominant genetic marker for sex identification was developed. • The sexing maker is not transferable even to closely related species, implying diversity in sex chromosomes among abalones.