Identification and mapping of sex-linked markers in giant abalone (Haliotis gigantea Gmelin)

• Published in: Aquaculture Vol. 595; p. 741529
• Main Authors: Tang, Chaonan, Luo, Hanjiao, Luo, Xuan, You, Weiwei, Ke, Yizhou, Ren, Peng, Ke, Caihuan, Cai, Mingyi
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 30.01.2025
• Subjects: Abalone; Sex determination system; Sex-linked marker; Whole genome sequencing; Sex determination system; Abalone; Sex-linked marker; Whole genome sequencing
• ISSN: 0044-8486
• DOI: 10.1016/j.aquaculture.2024.741529

Giant abalone (Haliotis gigantea Gmelin) is an economically important species within Haliotis genus, yet the genetic basis of sex in this species is still poorly understood. Therefore, we screened and mapped sex-linked SNPs and InDels, and subsequently developed a PCR-based method for genetic sex identification in giant abalone. Based on whole-genome sequencing reads, we obtained a total 6,159,941 high-quality SNPs and 2,623,263 high-quality InDels. Among them, 1,737 SNPs and 179 InDels were detected as sexually dimorphic, assuming a male heterogametic sex determination system. The majority of these variants, 99.1 % for SNPs and 99.4 % for InDels, were clustered on Chr.4 (0.02 Mb to 23.22 Mb). Furthermore, the estimation of genetic divergence between the sexes using FST showed that the genomic windows with the top 1 % FST values were concentrated on Chr.4 (0.5 Mb to 19.0 Mb) and Chr.5 (20.0 Mb to 35.0 Mb). Based on the sexually dimorphic variants on Chr.4, three PCR-based markers were successfully developed to determine the genetic sex of giant abalone. PCR validation using a tested panel of 67 females and 67 males from a cultivated population demonstrated compliance rates for these three markers ranging from 97.7 % to 99.3 %. These results suggest that the sex determination system is male heterogametic in giant abalone. Thus, this study provides valuable insights and tools for further research on the mechanisms of sex determination and differentiation, as well as for monitoring sex ratios in wild and cultivated populations in giant abalone. •Sex-linked SNPs/InDels were identified and mapped in giant abalone.•A PCR-based method for genetic sex identification was developed.•A male heterogametic sex determination system was revealed in giant abalone.