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Baker, J.; A’Hara, S.; Perry, A. ; Cottrell, J.; Ennos, R.; Green, S.; Cavers, S.

Common juniper single nucleotide polymorphism (SNP) and microsatellite (SSR) genotype data from individuals sampled from 18 natural UK populations in 2019

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This dataset is available under the terms of the Open Government Licence

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https://doi.org/10.5285/27e7df36-d689-4803-93b4-c15935693b83

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.

Publication date: 2024-11-11

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Format

Comma-separated values (CSV)

Spatial information

Study area

Spatial representation type

Tabular (text)

Spatial reference system

OSGB 1936 / British National Grid

Temporal information

Temporal extent

2019-01-01 to 2019-12-31

Provenance & quality

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.

Licensing and constraints

This dataset is available under the terms of the Open Government Licence

Cite this dataset as:

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

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