Perry, A.; Wachowiak, W.; Donnelly, K.; Cavers, S.

Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse

This dataset contains details of the phenotypes (height, bud set and budburst) and genotypes (via SNP array) of trees from a common garden multi-species pine (Pinus sylvestris, Pinus mugo and Pinus uncinata) glasshouse trial between 2010 and 2013.

Publication date: 2021-08-31

Get the data

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

Format of the data: Text

You must cite: Perry, A.; Wachowiak, W.; Donnelly, K.; Cavers, S. (2021). Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf

 

Where/When

Study area
Temporal extent
2010-01-01    to    2013-12-31

Provenance & quality

A common garden glasshouse trial was established in 2010 using seed from natural populations from three species of pine: Pinus sylvestris (SY), Pinus mugo (MU), Pinus uncinata (UN). Open-pollinated seeds were collected from three to five trees per population from twenty-eight natural populations in Europe covering the geographic range of each species. The collection consisted of thirteen populations of SY, nine MU, and six UN. The trial was divided into 25 randomized blocks with up to five families per population, of which the first 18 blocks were analysed by Wachowiak et al. (2018a).

Phenotypes (height, bud set and budburst) were assessed in the glasshouse during spring (budburst), autumn (bud set) and winter (height) between 2010 and 2013.

A subset of trees were selected to be genotyped using a multi-species SNP array. Trees were genotyped using a multi-species SNP array (Perry et al., 2020). DNA was extracted from needles using a Qiagen DNeasy 96 kit following the manufacturer’s instructions. Needles were dried on silica gel prior to extraction and DNA was quantified using a Qubit spectrophotometer to ensure a minimum standardized concentration of 35ng/µl. The quality of genomic DNA was also checked visually for fragmentation on 1 % agarose gel.

Genotyping was done at Edinburgh Genomics following DNA amplification, fragmentation, chip hybridisation, single-base extension through DNA ligation and signal amplification performed according to the Affymetrix Axiom® Assay protocol. Genotyping was performed in 384-well format on a GeneTitan according to the manufacturer’s procedure. Genotype calls were performed using Axiom Analysis Suite software as recommended by the manufacturer (ThermoFisher). Samples were assigned to an analysis group based on their call rate (CR) and dish QC (DQC: a metric provided by ThermoFisher which is generated by measuring signals at multiple sites in the genome known not to vary among individuals), using the following thresholds: DQC ‘high’ ≥ 0.82; DQC ‘low’ < 0.82; CR ‘high’ ≥ 96; CR ‘low’ < 96. Analyses: 1) DQC high + CR high; 2) DQC high + CR low; 3) DQC low + CR low. High quality samples (N=529), with high CR and DQC, were used to set thresholds for allele calls. Posteriors for allele calls were subsequently used as priors for analyses 2 (N = 753) and 3 (N = 251).

Correspondence/contact details

Perry, A.
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
 enquiries@ceh.ac.uk

Authors

Perry, A.
UK Centre for Ecology & Hydrology
Wachowiak, W.
Adam Mickiewicz University
Donnelly, K.
UK Centre for Ecology & Hydrology
Cavers, S.
UK Centre for Ecology & Hydrology

Other contacts

Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Biota
Keywords
budburst,  genotypes,  height,  Phenology,  Scots pine,  SNP array
INSPIRE Theme
Environmental Monitoring Facilities
Funding
Natural Environment Research Council Award: NE/K012177/1
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
18 May 2022 12:21