Identification

Title

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

Abstract

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

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/27e7df36-d689-4803-93b4-c15935693b83

name: Download the data

description: Download a copy of this data

function: download

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

Unique resource identifier

code

https://catalogue.ceh.ac.uk/id/27e7df36-d689-4803-93b4-c15935693b83

codeSpace

doi:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

Habitats and Biotopes

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Geographic location

West bounding longitude

-8.648

East bounding longitude

1.768

North bounding latitude

60.861

South bounding latitude

49.864

Temporal reference

Temporal extent

Begin position

2019-01-01

End position

2019-12-31

Dataset reference date

date type

publication

effective date

2024-11-11

date type

creation

effective date

2024-10-17

Frequency of update

Quality and validity

Lineage

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.

Conformity

Conformity report

specification

title

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

reference date

date type

publication

effective date

2010-12-08

degree

explanation

Data format

name of format

Comma-separated values (CSV)

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

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

Responsible organisations

Responsible party

organisation name

email address

enquiries@ceh.ac.uk

web address

https://orcid.org/0009-0003-0514-4644

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

email address

enquiries@ceh.ac.uk

web address

https://orcid.org/0009-0003-0514-4644

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

pointOfContact

Responsible party

organisation name

Forest Research

email address

stuart.ahara@forestresearch.gov.uk

web address

https://orcid.org/0000-0001-7891-4513

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

email address

enquiries@ceh.ac.uk

web address

https://orcid.org/0000-0002-7889-7597

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

Forest Research

email address

joan.cottrell@forestresearch.gov.uk

web address

https://orcid.org/0000-0001-6355-1326

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

University of Edinburgh

email address

rennos@ed.ac.uk

web address

https://orcid.org/0000-0001-5401-297X

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

Forest Research

email address

sarah.green@forestresearch.gov.uk

responsible party role

author

Responsible party

organisation name

email address

enquiries@ceh.ac.uk

web address

https://orcid.org/0000-0003-2139-9236

name: ORCID record

description: ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.

function: information

responsible party role

author

Responsible party

organisation name

email address

info@eidc.ac.uk

responsible party role

custodian

Responsible party

organisation name

email address

info@eidc.ac.uk

responsible party role

publisher

Responsible party

organisation name

email address

enquiries@ceh.ac.uk

responsible party role

owner

Metadata on metadata

Metadata point of contact

organisation name

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

UK

email address

info@eidc.ac.uk

web address

https://eidc.ac.uk/

name: EIDC website

description: The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences.

function: information

responsible party role

pointOfContact

Metadata date

2024-11-14T13:21:18

Metadata language

eng