Mapping and marker identification for sex-determining in the Pacific abalone, Haliotis discus hannai Ino

Abstract Pacific abalone (Haliotis discus hannai Ino) is an economically important mollusk. It has a male heterogametic (XX/XY) sex determination system. However, little is currently known on the molecular basis of sex determination in the species. Therefore, we identified the sex-linked genomic segment and markers with genome re-sequencing in Pacific abalone. A total of 8,473,763 high quality SNPs and 6,332,868 indels were obtained with resequencing and further processing. Among them, 2397 SNPs and 98 indels were detected as sexually dimorphic. According to distribution of sexually dimorphic SNPs, a major segment on Chr. 9 (~2.59 Mb) and a minor one on Chr.2 (~50.02 Kb) were identified as sex-linked, consistent to the results of genome-wide association analysis (GWAS). In addition, a diagnostic marker (MSP-2) for genetic sex of Pacific abalone was developed according to the male-specific deletion rs4391834 (12 bp). These results were useful in further researches on the molecular mechanism of sex determination and sex-control breeding in Pacific abalone.