Whole-Genome Re-Sequencing Identifies Male-Associated Markers and a Marker-Enriched Region on Chromosome 14 in Siniperca scherzeri.
- 1Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
- 2Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Jiaxing 314006, China.
- 3School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China.
Abstract
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.
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BibTeX
@article{zheng2026wholegenome,
title = {{Whole-Genome Re-Sequencing Identifies Male-Associated Markers and a Marker-Enriched Region on Chromosome 14 in Siniperca scherzeri.}},
author = {Jianbo Zheng and Xiaohai Zhang and Xiaohui Xu and Shili Liu and Wenping Jiang and Chao Zhu and Cancan Huang and Fei Li},
journal = {Biology},
year = {2026},
month = sep,
doi = {10.3390/biology15191675},
url = {https://europepmc.org/article/MED/42883348},
note = {CC BY},
}
RIS
TY - JOUR
TI - Whole-Genome Re-Sequencing Identifies Male-Associated Markers and a Marker-Enriched Region on Chromosome 14 in Siniperca scherzeri.
AU - Jianbo Zheng
AU - Xiaohai Zhang
AU - Xiaohui Xu
AU - Shili Liu
AU - Wenping Jiang
AU - Chao Zhu
AU - Cancan Huang
AU - Fei Li
PY - 2026
DA - 2026/09/22
JO - Biology
DO - 10.3390/biology15191675
UR - https://europepmc.org/article/MED/42883348
AB - 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.
SN - 2079-7737
ER -