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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
Identifier
https://catalogue.ceh.ac.uk/id/27e7df36-d689-4803-93b4-c15935693b83
Identifier
doi: / 10.5285/27e7df36-d689-4803-93b4-c15935693b83
Other citation details
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
Author
  UK Centre for Ecology & Hydrology - Baker, J.
https://orcid.org/0009-0003-0514-4644
Point of contact
  UK Centre for Ecology & Hydrology - Baker, J.
https://orcid.org/0009-0003-0514-4644
Author
  Forest Research - A’Hara, S.
https://orcid.org/0000-0001-7891-4513
Author
  UK Centre for Ecology & Hydrology - Perry, A.
https://orcid.org/0000-0002-7889-7597
Author
  Forest Research - Cottrell, J.
https://orcid.org/0000-0001-6355-1326
Author
  University of Edinburgh - Ennos, R.
https://orcid.org/0000-0001-5401-297X
Author
  Forest Research - Green, S.
Author
  UK Centre for Ecology & Hydrology - Cavers, S.
https://orcid.org/0000-0003-2139-9236
Custodian
  NERC EDS Environmental Information Data Centre
Publisher
  NERC EDS Environmental Information Data Centre
Owner
  UK Centre for Ecology & Hydrology
GEMET - INSPIRE themes, version 1.0
  • Habitats and Biotopes
Access constraints
otherRestrictions Other restrictions
Other constraints
no limitations
Use constraints
otherRestrictions Other restrictions
Other constraints
This resource is available under the terms of the Open Government Licence
Use constraints
otherRestrictions Other restrictions
Other constraints
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
textTable Text, table
Distance
10  urn:ogc:def:uom:EPSG::9001
Metadata language
EnglishEnglish
Character set
utf8 UTF8
Topic category
  • Biota
Begin date
2019-01-01
End date
2019-12-31
N
S
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W
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Unique resource identifier
OSGB 1936 / British National Grid
Distribution format
  • Comma-separated values (CSV) ()

Distributor
  NERC EDS Environmental Information Data Centre
OnLine resource
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Hierarchy level
dataset Dataset
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dataset

Conformance result

Date (Publication)
2010-12-08
Statement
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.
File identifier
27e7df36-d689-4803-93b4-c15935693b83 XML
Metadata language
EnglishEnglish
Character set
ISO/IEC 8859-1 (also known as Latin 1) 8859 Part 1
Hierarchy level
dataset Dataset
Hierarchy level name
dataset
Date stamp
2025-03-23T12:56:16
Metadata standard name
UK GEMINI
Metadata standard version
2.3
Point of contact
  NERC EDS Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK
https://eidc.ac.uk/
 
 

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Keywords

GEMET - INSPIRE themes, version 1.0
Habitats and Biotopes

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