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
dataset
https://data-package.ceh.ac.uk/data/27e7df36-d689-4803-93b4-c15935693b83
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https://data-package.ceh.ac.uk/sd/27e7df36-d689-4803-93b4-c15935693b83.zip
name: Supporting information
description: Supporting information available to assist in re-use of this dataset
function: information
https://catalogue.ceh.ac.uk/id/27e7df36-d689-4803-93b4-c15935693b83
doi:
eng
biota
Habitats and Biotopes
publication
2008-06-01
-8.648
1.768
60.861
49.864
2019-01-01
2019-12-31
publication
2024-11-11
creation
2024-10-17
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.
publication
2010-12-08
Comma-separated values (CSV)
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
https://orcid.org/0009-0003-0514-4644
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https://orcid.org/0009-0003-0514-4644
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pointOfContact
Forest Research
stuart.ahara@forestresearch.gov.uk
https://orcid.org/0000-0001-7891-4513
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https://orcid.org/0000-0002-7889-7597
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author
Forest Research
joan.cottrell@forestresearch.gov.uk
https://orcid.org/0000-0001-6355-1326
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author
University of Edinburgh
https://orcid.org/0000-0001-5401-297X
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author
Forest Research
sarah.green@forestresearch.gov.uk
author
https://orcid.org/0000-0003-2139-9236
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Lancaster Environment Centre, Library Avenue, Bailrigg
Lancaster
LA1 4AP
UK
name: EIDC website
description: The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences.
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2024-11-14T13:21:18