Whole-Genome Re-Sequencing Identifies Male-Associated Markers and a Marker-Enriched Region on Chromosome 14 in Siniperca scherzeri

Sex-specific markers are important for genetic sex identification and sex-control breeding in aquaculture. Siniperca scherzeri (Steindachner, 1892) is an economically important freshwater fish with female-biased sexual size dimorphism, but its sex-associated genomic architecture remains poorly characterized. Here, whole-genome resequencing of 10 females and 10 males generated approximately 480 Gb of clean data and identified 55 candidate male-associated fragments using a read-presence/absence screening strategy. PCR testing identified seven candidate male-associated markers that showed male-specific amplification and complete concordance with phenotypic sex in the tested S. scherzeri cohort. Marker4, Marker5, and Marker18 showed the same amplification pattern in the tested Siniperca chuatsi (Basilewsky, 1855) and Siniperca knerii (Garman, 1912) samples. The seven amplicons mapped to a marker-enriched interval at 20.677–20.695 Mb on chromosome 14. Marker18 overlapped a partial candidate amh-family gene model; however, no male-specific sequence variant, sex-biased expression, or functional role was tested. Because all S. scherzeri samples originated from one farmed cohort of unknown pedigree and the PCR assays lacked dedicated no-template and internal amplification controls, the observed concordance should not be interpreted as established diagnostic performance. The data support a male-associated marker cluster on chromosome 14, rather than establishing a Y-specific sex-determining region or a differentiated sex chromosome. Independent population validation with appropriate assay controls, together with genome-wide structural, expression, and functional analyses, is required.