Sex-specific loci are powerful tools for identifying sex determination systems. They offer a molecular biotechnological approach for producing all‐male or all-female fish for commercial breeding. The North African catfish has been widely adopted for aquaculture, because its superior growth and disease resistance render the species suitable for hybridization with other catfish, to improve the productivity and quality of fish meat. North African catfish have either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing. This approach was effective for identifying sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 phenotypic sex assignments of North African catfish. In total, 41 male-linked loci met the criteria of moderately sex-linked loci (70:30, male:female; 80:20, male:female). By contrast, only 25 female-linked loci were detected from moderately sex-linked loci, and no perfectly male- or female-specific sex-linked loci were observed. Several male-linked loci were partially homologous to transposable element and functional genes, and most also showed partial homology with several amniote sex chromosomal linkages. This suggests that an ancestral amniote super-sex chromosome with overlaps of partial sex chromosomal linkages was also found in teleosts, and that the male heterogametic XX/XY sex determination system should exist in North African catfish. The putative Y chromosome is young and the non-recombination region is highly cryptic. In addition, the ZW type of North African catfish exhibits heteromorphic sex chromosomes, whereas the two other groups of North African catfish have different sex determination systems. Thus, turnover of sex chromosome systems might have occurred stochastically in ancestral homomorphic sex chromosomes. The XY group has been introduced into Thailand for commercial breeding. This approach using sex-specific loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.

Adult individuals, 15 male and 15 female African catfish, were sampled. The individuals were selected randomly from a large breeding stock (Kasetsart University, Bangkok, Thailand) to avoid the possibility of a high incidence of siblings in our genetic pool. The sex of each individual was determined based on external morphology and internal examination of gonadal morphology (Esmaeili et al., 2017; Ponjarat et al., 2019). The dorsal fins were then removed for DNA extraction. The following analyses were performed: total genomic DNA, DArT sequencing and genotyping, marker selection and DArT sequencing analysis, comparison of potential sex-linked loci, and homology searching