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Divergent pattern between phenotypic and genetic variation in Scots pine

SND-ID: 2020-208

Overview
Data and documentation

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Jenny Olsson - Umeå University, Ecology and Environmental Science

Wei Zhao - Umeå University, Ecology and Environmental Science

Johan Kroon - Forestry Research Institute of Sweden

Ulfstand Wennström - Forestry Research Institute of Sweden

Description

In this study, we sampled 54 Scots pine populations from the Norwegian coast over the Arctic Circle to western Russia covering 47.3 longitudes or more than 1/8th of the earth’s circumference, which represents the most comprehensive coverage of Northern Europe to date. We inferred variation in autumn phenology and dormancy progression from freeze hardiness tests conducted on >5000 seedlings, of which >900 seedlings from 24 populations were genotyped using genotyping-by-sequencing (GBS). Our main goal was to evaluate adaptive responses in Scots pine at phenotype and genotype levels. Evaluation of cold hardiness along environmental and geographical gradients would contribute to an understanding of the performance of these gradients for predicting freeze damage levels. The genotype data allow evaluation of genetic variance across landscapes and thus shed light on the degree of genetic-environmental association and the recolonization history of Scots pine in Scandinavia.

Language

English

Research principal, contributors, and funding

Research principal

Umeå University

Responsible department/unit

Ecology and Environmental Science

Protection and ethical review

Data contains personal data

Method and time period

Time period(s) investigated

1985 – 2017

Geographic coverage

Geographic spread

Geographic location: Northern Europe

Geographic description: Data from Scots pine seeds collected from Norway, Sweden, Finland, Arkhangelsk- och Komi- regions of Russia

Topic and keywords

Research area

Bioinformatics (Computational Biology), Genetics, Evolutionary Biology, Forest Science (The Swedish standard of fields of research 2011)
Biota, Geoscientific Information, Environment, Location (INSPIRE topic categories)

Keywords

genetic population structure, population structure, population genetics, habitats and biotopes, species distribution, gbs, pinus sylvestris, scots pine

Publications

Hall et al. 2021. Divergent pattern between phenotypic and genetic variation in Scots pine. Plant Communications
DOI: https://doi.org/10.1016/j.xplc.2020.100139

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Dataset 1

935 genotyped from 24 populations of Pinus sylvestris across Northern Europe

Download data

All_individuals_935.vcf.gz (58.86 MB)

Associated documentation

Data description and analysis_Bookmarks.pdf

Data description and analysis_Archive.pdf

Description

SNP data of Pinus sylvestris from geneotyping-by-sequencing, Sequenced by Illumina HiSeq X. Text file as gzipped vcf (.vcf.gz). See "pheno_pop.txt" for information on each individual.

Version 1

2021-01-29
https://doi.org/10.5878/8bg9-ah89

Citation

David Hall. Umeå University (2021). 935 genotyped from 24 populations of Pinus sylvestris across Northern Europe. Swedish National Data Service. Version 1. https://doi.org/10.5878/8bg9-ah89

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Data format / data structure

Text

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Keywords

genetic population structure, population structure, population genetics, gbs, pinus sylvestris, scots pine

Variables

11039

License

Dataset 2

746 unrelated genotyped Pinus sylvestris from 24 different populations across Northern Europe

Download data

Unrelated_individuals_746.vcf.gz (47.33 MB)

Associated documentation

Data description and analysis_Bookmarks.pdf

Data description and analysis_Archive.pdf

Description

Text file as gzipped vcf (.vcf.gz). See "pheno_pop.txt" for more information on each individual.

Version 1

2021-01-29
https://doi.org/10.5878/rjzz-jk23

Citation

David Hall. Umeå University (2021). 746 unrelated genotyped Pinus sylvestris from 24 different populations across Northern Europe. Swedish National Data Service. Version 1. https://doi.org/10.5878/rjzz-jk23

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Data format / data structure

Text

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Keywords

genetic population structure, population structure, population genetics, gbs, pinus sylvestris, scots pine

Variables

10925

License

Dataset 3

Phenotype estimates of the genotyped individuals

Download data

pheno_pop.txt (20.54 KB)

Associated documentation

Data description and analysis_Bookmarks.pdf

Data description and analysis_Archive.pdf

Description

The phenotypes of all genotyped individuals. Includes each individuals population number and seedlot

Version 1

2021-01-29
https://doi.org/10.5878/0msc-3v36

Citation

David Hall. Umeå University (2021). Phenotype estimates of the genotyped individuals. Swedish National Data Service. Version 1. https://doi.org/10.5878/0msc-3v36

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Data format / data structure

Numeric

Text

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Keywords

genetic population structure, population structure, population genetics, gbs, pinus sylvestris, scots pine

Variables

License

Dataset 4

Environmental variables and coordinates for each population

Download data

pop_env.txt (39.57 KB)

Associated documentation

Data description and analysis_Bookmarks.pdf

Data description and analysis_Archive.pdf

Description

Environmental variables for each population was extracted based on their latitude and longitude at origin from 68 different high resolution environmental grids. These variables were then used for phenotype- and genotype-environment association analyses. A description of all variables can be found in Table S2 in “Document S1. Supplemental methods, Supplemental Figures 1–4, and Supplemental Tables 1–6.”, available from doi.org/10.1016/j.xplc.2020.100139

Version 1

2021-01-29
https://doi.org/10.5878/45yn-ag55

Citation

David Hall. Umeå University (2021). Environmental variables and coordinates for each population. Swedish National Data Service. Version 1. https://doi.org/10.5878/45yn-ag55

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Data format / data structure

Numeric

Text

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Keywords

genetic population structure, population structure, population genetics, gbs, pinus sylvestris, scots pine

Variables

License

Dataset 5

Results from seedlings exposure to freezing temperatures

Download data

freeze_res.txt (650.78 KB)

Associated documentation

Data description and analysis_Bookmarks.pdf

Data description and analysis_Archive.pdf

Description

The resulting damage levels (Damage) from exposing seedlings to freezing temperature. The damage levels were scored between 1 to two weeks after exposure to allow discoloration. A 0 damage level meant no discoloration while 6 was completely discolored or dead. Damage levels were rank normalized (DamageN) across replications (Repl).

Version 1

2021-01-29
https://doi.org/10.5878/7pt2-ja36

Citation

David Hall. Umeå University (2021). Results from seedlings exposure to freezing temperatures. Swedish National Data Service. Version 1. https://doi.org/10.5878/7pt2-ja36

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Data format / data structure

Numeric

Text

Creator/Principal investigator(s)

David Hall - Umeå University, Ecology and Environmental Science

Keywords

genetic population structure, population structure, population genetics, gbs, pinus sylvestris, scots pine

Variables

License

Published: 2021-01-29

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