BGS Hosted Metadata
Common juniper single nucleotide polymorphism (SNP) and microsatellite (SSR) genotype data from individuals sampled from 18 natural UK populations in 2019
This dataset contains genotype data of Single Nucleotide Polymorphisms (SNPs) and Simple Sequence Repeats (SSRs) from 18 populations of UK juniper, including the two subspecies hemisphaerica and nana. Plant material was collected in 2019. These data were gathered as part of a project on juniper conservation genetics that also includes an analysis of the quantitative genetics of UK junipers. The main goal of the project is to evaluate the standing genetic variation of populations using both quantitative and population genetic analyses. Full details about this dataset can be found at https://doi.org/10.5285/27e7df36-d689-4803-93b4-c15935693b83
Simple
- Date (Publication)
- 2024-11-11
- Date (Creation)
- 2024-10-17
- Citation identifier
- https://catalogue.ceh.ac.uk/id/27e7df36-d689-4803-93b4-c15935693b83
- Citation identifier
- doi: / 10.5285/27e7df36-d689-4803-93b4-c15935693b83
- Other citation details
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Baker, J., A’Hara, S., Perry, A., Cottrell, J., Ennos, R., Green, S., Cavers, S. (2024). Common juniper single nucleotide polymorphism (SNP) and microsatellite (SSR) genotype data from individuals sampled from 18 natural UK populations in 2019. NERC EDS Environmental Information Data Centre 10.5285/27e7df36-d689-4803-93b4-c15935693b83
- Point of contact
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Organisation name Individual name Electronic mail address Role UK Centre for Ecology & Hydrology Baker, J. Author UK Centre for Ecology & Hydrology Baker, J. Point of contact Forest Research A’Hara, S. Author UK Centre for Ecology & Hydrology Perry, A. Author Forest Research Cottrell, J. Author University of Edinburgh Ennos, R. Author Forest Research Green, S.
Author UK Centre for Ecology & Hydrology Cavers, S. Author NERC EDS Environmental Information Data Centre Custodian NERC EDS Environmental Information Data Centre Publisher UK Centre for Ecology & Hydrology Owner
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GEMET - INSPIRE themes, version 1.0
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Habitats and Biotopes
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Wikidata
- Keywords
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- Biodiversity
- population genetics
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Britain
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juniper
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genetic data
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SNP
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SSR
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neutral genetic variation
- Access constraints
- Other restrictions
- Other constraints
- no limitations
- Use constraints
- Other restrictions
- Use constraints
- Other restrictions
- Other constraints
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If you reuse this data, you should cite: Baker, J., A’Hara, S., Perry, A., Cottrell, J., Ennos, R., Green, S., Cavers, S. (2024). Common juniper single nucleotide polymorphism (SNP) and microsatellite (SSR) genotype data from individuals sampled from 18 natural UK populations in 2019. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/27e7df36-d689-4803-93b4-c15935693b83
- Spatial representation type
- Text, table
- Distance
- 10 urn:ogc:def:uom:EPSG::9001
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
- Begin date
- 2019-01-01
- End date
- 2019-12-31
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- Unique resource identifier
- OSGB 1936 / British National Grid
- Distribution format
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Name Version Comma-separated values (CSV)
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/27e7df36-d689-4803-93b4-c15935693b83 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/27e7df36-d689-4803-93b4-c15935693b83.zip Supporting information
- Hierarchy level
- Dataset
- Other
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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For the SNP genotyping plant material was collected in 2019. Needles were freeze-dried and finely chopped using a razor blade, and then using a Retsch MM 300 mixer mill at a frequency of 30/s for a total of 2 minutes with metal beads in each Eppendorff tube to grind samples. Razor blades, scissors and lab surfaces were cleaned with 2% ethanol between processing samples. DNA was extracted for each sample using a Qiagen DNeasy Plant Pro kit following the manufacturer’s instructions. SNPs were identified and sequenced for this study by the Plant Genomic Resources Centre (CNRGV, INRAE, France; https://cnrgv.toulouse.inrae.fr/). A sub-sample of these were used to develop two Sequenom SNP chips which provided data on 74 SNP loci in the samples analysed in this study For the SSR genotyping a new set of microsatellite markers was developed for this study. Juniper DNA samples were sent to Microsynth Ecogenics ( https://www.ecogenics.ch/home.html) to identify nuclear microsatellite (SSR) polymorphisms. Of the 285 identified microsatellites 48 were tested using multiplex PCR and gel electrophoresis which returned 6 polymorphic markers which were consistently amplified by PCR. PCR products were run on a Licor 4300 DNA sequencer and the allele sizes scored by eye using a size marker as reference.
Metadata
- File identifier
- 27e7df36-d689-4803-93b4-c15935693b83 XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-11-13T16:15:02
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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