Colinearity based sex-specific marker development in the golden pompano (Trachinotus ovatus)

Abstract

The golden pompano, Trachinotus ovatus, is a promising species in the mariculture. However, the sex identification in alive individual is a bottleneck step in selective breeding. The golden pompano and the greater amberjack, Seriola dumerili, belong to the same family, Carangidae. The genome assembly of golden pompano has been released and the sex determining mechanism in the greater amberjack has been deeply understood. The genome assembly of the golden pompano was improved with Hi-C sequencing and the presumed sex determining region was detected by aligning with the sex determining region of the greater amberjack. A SNP (Chr17:8325779) within the gene Hsd17b1 was successfully converted into a sex-specific marker that can be genotyped by kompetitive allele specific PCR and high resolution melting analysis with 100% the accuracy of sex identification. The results that only one presumed sex determining region was detected with gene Hsd17b1 lied in and the genotype of the developed sex-specific marker was heterozygous in female and homozygous in male supported the sex chromosome system was ZZ/ZW and the candidate sex determining gene was Hsd17b1. The results would benefit the selective breeding program of the golden pompano.