Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic mic...

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Autores principales: Wang, Huaying, Yang, Baiming, Wang, Huan, Xiao, Hongxing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060317/
https://www.ncbi.nlm.nih.gov/pubmed/33883608
http://dx.doi.org/10.1038/s41598-021-87945-x
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author Wang, Huaying
Yang, Baiming
Wang, Huan
Xiao, Hongxing
author_facet Wang, Huaying
Yang, Baiming
Wang, Huan
Xiao, Hongxing
author_sort Wang, Huaying
collection PubMed
description Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.
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spelling pubmed-80603172021-04-23 Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species Wang, Huaying Yang, Baiming Wang, Huan Xiao, Hongxing Sci Rep Article Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species. Nature Publishing Group UK 2021-04-21 /pmc/articles/PMC8060317/ /pubmed/33883608 http://dx.doi.org/10.1038/s41598-021-87945-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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 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/) .
spellingShingle Article
Wang, Huaying
Yang, Baiming
Wang, Huan
Xiao, Hongxing
Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title_full Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title_fullStr Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title_full_unstemmed Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title_short Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species
title_sort impact of different numbers of microsatellite markers on population genetic results using slaf-seq data for rhododendron species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060317/
https://www.ncbi.nlm.nih.gov/pubmed/33883608
http://dx.doi.org/10.1038/s41598-021-87945-x
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