Sex-linked DNA marker screening and characterization in albino northern snakehead (Channa argus var.) via third-generation sequencing and pool resequencing

The northern snakehead (Channa argus) exhibits male heterogamety (XY/XX), as well as sexually dimorphic growth rate. Within this species, males generally grow more quickly than females. Breeding all-male (XY) populations is preferred for large-scale fish culture. In this study, Hi-C and Nanopore sequencing methods were utilized to produce a chromosome-level genome for an albino XY C. argus var. The size of genome assembly was 0.66 GB, the contig N50 length was 13.64 Mb, and the scaffold N50 length was 28.14 Mb. 24 chromosomes, assembled from the XY genome, exhibited complete concordance with the XX genome in a synteny analysis. We also sequenced a male pool (15 albino male fish) and a female pool (15 albino female fish) by Illumina high-throughput sequencing. Mapping of the resequencing data to the XX and XY genome assembly enabled us to identify the sex chromosome (Chr16) and the 1.04 Mb (from 10.99 to 12.03 Mb) sex-determining region (SDR). Five sex-linked DNA markers were identified by screening the structural variations in the SDR. Marker-1 and Marker-2 were co-dominant markers, while Markers 3–5 were Y-linked markers. These markers could distinguish the genetic sex (XX, XY and YY genotype) of C. argus var. with a 100% concordance rate. Importantly, these markers also worked in farmed and wild populations of C. argus. Subsequently, YY super-males produced from crosses between XY males (♂) and XY neofemales (♀) were identified, using these sex-linked markers. By comparing the SDR sequences of XX and XY, one X-linked marker was identified that amplified X-specific bands in XX and XY, but not in YY individuals, which can be used to further confirm the YY genotype. This study provides a high quality XY genome, and a PCR-based technique for determining the genetic sex of snakeheads, which can be used to promote all-male snakehead production.