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A 13-plex of tetra- and penta-STRs to identify zebrafish
The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052278/ https://www.ncbi.nlm.nih.gov/pubmed/32123258 http://dx.doi.org/10.1038/s41598-020-60842-5 |
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author | Venta, Patrick J. Nguyen, Anthony K. Senut, Marie-Claude Poulos, William G. Prukudom, Sukumal Cibelli, Jose B. |
author_facet | Venta, Patrick J. Nguyen, Anthony K. Senut, Marie-Claude Poulos, William G. Prukudom, Sukumal Cibelli, Jose B. |
author_sort | Venta, Patrick J. |
collection | PubMed |
description | The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage (“stutter”) that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10(−5) and the PI for siblings (PIsib) was 6.4 × 10(−3), as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model. |
format | Online Article Text |
id | pubmed-7052278 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70522782020-03-11 A 13-plex of tetra- and penta-STRs to identify zebrafish Venta, Patrick J. Nguyen, Anthony K. Senut, Marie-Claude Poulos, William G. Prukudom, Sukumal Cibelli, Jose B. Sci Rep Article The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage (“stutter”) that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10(−5) and the PI for siblings (PIsib) was 6.4 × 10(−3), as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model. Nature Publishing Group UK 2020-03-02 /pmc/articles/PMC7052278/ /pubmed/32123258 http://dx.doi.org/10.1038/s41598-020-60842-5 Text en © The Author(s) 2020 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Venta, Patrick J. Nguyen, Anthony K. Senut, Marie-Claude Poulos, William G. Prukudom, Sukumal Cibelli, Jose B. A 13-plex of tetra- and penta-STRs to identify zebrafish |
title | A 13-plex of tetra- and penta-STRs to identify zebrafish |
title_full | A 13-plex of tetra- and penta-STRs to identify zebrafish |
title_fullStr | A 13-plex of tetra- and penta-STRs to identify zebrafish |
title_full_unstemmed | A 13-plex of tetra- and penta-STRs to identify zebrafish |
title_short | A 13-plex of tetra- and penta-STRs to identify zebrafish |
title_sort | 13-plex of tetra- and penta-strs to identify zebrafish |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7052278/ https://www.ncbi.nlm.nih.gov/pubmed/32123258 http://dx.doi.org/10.1038/s41598-020-60842-5 |
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