Sex-specific markers developed by next-generation sequencing confirmed a male heterogametic sex determination in small abalone, Haliotis diversicolor

Abstract

Small abalone (Haliotis diversicolor) is an economically important shellfish in aquaculture, yet its sex determination mechanism remains unclear. Based on the re-sequencing data, candidate sexually dimorphic loci, including 281 SNPs and 21 InDels, were screened out in small abalone. The candidate sexually dimorphic SNPs were located on thirteen chromosomes but mainly on Chr. 3 (43.4%) and Chr. 9 (26.7%); while the candidate sexually dimorphic InDels were located on six chromosomes and also mainly on Chr. 3 (38.1%) and Chr. 9 (26.7%). After being checked with Integrative Genomic Viewer (IGV) and PCR, a dominant marker (SD3) based on three consecutive sexually dimorphic SNPs on Chr. 3 and a codominant marker (SC9) based on a male-specific deletion on Chr. 9 were developed to distinguish the genetic sex in small abalone. PCR validation gained 100% consistence for both sex-specific markers in the progenies of Taiwan population and an intra-hybrid variety with male parents originated from Tokyo population. The successful development of the male-specific markers suggested that small abalone has a male heterogametic sex determination and may have two sex-linked chromosomes, and also provided important tools and clues for further studies on mechanism of sex determination in small abalone.