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Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)

BACKGROUND: The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification metho...

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Autores principales: Xing, Teng-Fei, Li, Yu-Long, Liu, Jin-Xian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254354/
https://www.ncbi.nlm.nih.gov/pubmed/34215185
http://dx.doi.org/10.1186/s12864-021-07830-9
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author Xing, Teng-Fei
Li, Yu-Long
Liu, Jin-Xian
author_facet Xing, Teng-Fei
Li, Yu-Long
Liu, Jin-Xian
author_sort Xing, Teng-Fei
collection PubMed
description BACKGROUND: The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. RESULTS: Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. CONCLUSIONS: The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07830-9.
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spelling pubmed-82543542021-07-06 Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius) Xing, Teng-Fei Li, Yu-Long Liu, Jin-Xian BMC Genomics Research BACKGROUND: The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. RESULTS: Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. CONCLUSIONS: The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07830-9. BioMed Central 2021-07-02 /pmc/articles/PMC8254354/ /pubmed/34215185 http://dx.doi.org/10.1186/s12864-021-07830-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Xing, Teng-Fei
Li, Yu-Long
Liu, Jin-Xian
Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title_full Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title_fullStr Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title_full_unstemmed Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title_short Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius)
title_sort female-specific genomic regions and molecular sex identification of the clearhead icefish (protosalanx hyalocranius)
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254354/
https://www.ncbi.nlm.nih.gov/pubmed/34215185
http://dx.doi.org/10.1186/s12864-021-07830-9
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