Development of sex-specific markers in Spinyhead croaker, Collichthys lucidus

Spinyhead croaker (Collichthys lucidus) is a commercially important marine sciaenid fish, being found diverging into northern and southern lineages. A sex diagnostic marker has been developed in the croaker, but its application scope was limited in the populations belonging to southern lineage. In present study, novel diagnostic markers were developed to break the limitation. Resequencing was performed with samples from Zhousan (ZS) population and Ningde (ND), representing northern and southern lineages respectively. Based on the resulted data, the candidate sexually dimorphic SNPs and InDels were screened out, and their genomic distributions were visualized. For ZS population, 52,621 SNPs and 8594 InDels were screened out, mainly distributing on Chr.1 and Chr.8 along almost entire chromosome. For ND population, 2094 SNPs and 350 InDels were screened out, mainly clustering within a 0.55-Mb segment from 4.31–4.86 Mb on Chr.1 and a 1.58-Mb segment from 27.12–28.70 Mb on Chr.7. Based on a common male-specific delete on Chr.1, PCR primer pair CMS-1 was designed and demonstrated applicable to all four tested populations covering both lineages; while based on a male-specific delete of Chr.8 for ZS population, PCR primer pair ZS-8 was designed and demonstrated applicable only to the northern populations but not the southern populations. The novel sex-specific markers developed in the present study extend the toolkit for both sex control breeding and basic study on sex determination in the croaker. Besides, different number and location of sexually dimorphic SNPs/InDels between two lineages provide new insights in sex chromosome evolution in spinyhead croaker.