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First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach

BACKGROUND: The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panel...

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Autores principales: Scarpulla, Erminia, Boattini, Alessio, Cozzo, Mario, Giangregorio, Patrizia, Ciucci, Paolo, Mucci, Nadia, Randi, Ettore, Davoli, Francesca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371798/
https://www.ncbi.nlm.nih.gov/pubmed/34407764
http://dx.doi.org/10.1186/s12864-021-07915-5
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author Scarpulla, Erminia
Boattini, Alessio
Cozzo, Mario
Giangregorio, Patrizia
Ciucci, Paolo
Mucci, Nadia
Randi, Ettore
Davoli, Francesca
author_facet Scarpulla, Erminia
Boattini, Alessio
Cozzo, Mario
Giangregorio, Patrizia
Ciucci, Paolo
Mucci, Nadia
Randi, Ettore
Davoli, Francesca
author_sort Scarpulla, Erminia
collection PubMed
description BACKGROUND: The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. RESULTS: We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. CONCLUSIONS: The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07915-5.
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spelling pubmed-83717982021-08-18 First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach Scarpulla, Erminia Boattini, Alessio Cozzo, Mario Giangregorio, Patrizia Ciucci, Paolo Mucci, Nadia Randi, Ettore Davoli, Francesca BMC Genomics Methodology Article BACKGROUND: The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes. RESULTS: We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping. CONCLUSIONS: The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07915-5. BioMed Central 2021-08-18 /pmc/articles/PMC8371798/ /pubmed/34407764 http://dx.doi.org/10.1186/s12864-021-07915-5 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 Methodology Article
Scarpulla, Erminia
Boattini, Alessio
Cozzo, Mario
Giangregorio, Patrizia
Ciucci, Paolo
Mucci, Nadia
Randi, Ettore
Davoli, Francesca
First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title_full First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title_fullStr First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title_full_unstemmed First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title_short First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach
title_sort first core microsatellite panel identification in apennine brown bears (ursus arctos marsicanus): a collaborative approach
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371798/
https://www.ncbi.nlm.nih.gov/pubmed/34407764
http://dx.doi.org/10.1186/s12864-021-07915-5
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