Identification of male sex-specific markers using genome re-sequencing in the Chinese longsnout catfish Leiocassis longirostris

The Chinese longsnout catfish (Leiocassis longirostris Gunther), an indigenous commercially important fish species in China, exhibits markedly sex dimorphism in growth, which the males grow much faster than females. So, we aimed to develop sex-specific DNA markers to accelerate the development of sex control techniques for L. longirostris. In this study, 15 individuals of each sex were sequenced using whole-genome re-sequencing technology. A total of 238.51 Gb clean data was used to detect the sex associated markers and we found that 2472 loci were enriched in the first 18 Mb of Chr 7, the putative sex-determination region for L. longirostris. All candidate markers were male heterozygous, implying that the sex-determination system of the L. longirostris is the XX/XY type. Using the sequence polymorphism of male and female individuals in this region, we designed six pairs of primers to develop sex-specific markers, of which three markers exclusively exhibited male-specific bands. Further validation showed that the accuracy of sex prediction was up to 100% for individuals in the Meishan, Chengdu, Yibin and Shishou regions, suggesting wide applicability among local populations. Importantly, marker 3 was located in the ACAP1 gene, which may be involved in sex determination or differentiation of L. longirostris. This method for developing sex-specific markers is efficient, simple, and provides a useful reference that can be applied to other fish species. The markers developed in this work could be instrumental for sex control breeding to increase the yield in the L. longirostris aquaculture industry.