Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray
bibliographic citation: Cavers, S., Wachowiak, W., Perry, A. (2020). Conversion rate, frequency and state of single nucleotide polymorphism loci for Scots pine Axiom microarray. NERC Environmental Information Data Centre. https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
description: The data comprise summary statistics for performance of a genotyping microarray for a test set of 87 samples for four pine species. The summary statistics comprise state (polymorphic, monomorphic), mean allele frequency and conversion rate, estimated for each locus as a mean across 87 sample genotypes. The array comprised 49,829 SNPs (single nucleotide polymorphisms) from several sources. The majority (N = 49,052) were obtained from transcriptome sequencing of four pine species: Pinus sylvestris, Pinus mugo, Pinus uncinata and Pinus uliginosa. The SNP set was filtered by the array manufacturer (Thermo Fisher) based on p-convert values signifying the SNP array quality, and a list of recommended and non-recommended SNP probes (avoiding SNPs with polymorphisms within 35 bp) was provided to the authors. These included SNPs that were common to all species and also SNPs fixed in one species and polymorphic within and among others. A further set of SNPs (N = 578) were included from candidate genes (N = 279), which had been resequenced in previous population genetic studies of the pine species. Variation in mitochondrial DNA (mtDNA) was targeted by inclusion of a set of mtDNA- specific SNPs (N = 14). Finally, a set of SNPs putatively associated with susceptibility to Dothistroma needle blight (discovered in Pinus radiata, European Nucleotide Archive accession numbers ERS1034542-53) were also included (N = 185).
provenance: ProvenanceStatement
  label: The dataset is a list of 49,829 SNP loci, identified by individual code with accompanying columns of basic information and statistics (Conversion type (Poly - polymorphic, Mono-monomorphic), mean allelic frequency (MAF), and call rate (CR)).
spatial: Location
publisher: NERC Environmental Information Data Centre
is referenced by: https://doi.org/10.1111/1755-0998.13223
subject: Pinus sylvestris
subject: Pinus mugo
subject: Pinus uliginosa
subject: Pinus uncinata
subject: Genomics
subject: Microarray
subject: SNPs
subject: Polymorphism
subject: Divergence
subject: Natural selection
subject: Speciation
subject: conifer
type: Dataset
available: 2020-06-26
landing page: https://doi.org/10.5285/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
license: OGL-UK-3.0.ttl
access rights: UNRS
distribution:
  access URL: https://data-package.ceh.ac.uk/data/0ba33e96-67cb-4650-b2bd-6ee13fa7de97
  license: OGL-UK-3.0.ttl
  access rights: UNRS
  format: Plain text
creator: Cavers, S.
creator: Wachowiak, W.
creator: Perry, A.
language: en

Cavers, S.
type: Person
family name: Cavers
given name: Stephen
member: UK Centre for Ecology & Hydrology

NERC Environmental Information Data Centre
type: Organization

Cavers, S.
type: Person
family name: Cavers
given name: S.
member: UK Centre for Ecology & Hydrology

Wachowiak, W.
type: Person
family name: Wachowiak
given name: W.
member: Adam Mickiewicz University

Perry, A.
type: Person
family name: Perry
given name: A.
member: UK Centre for Ecology & Hydrology

https://doi.org/10.1111/1755-0998.13223
type: Expression
bibliographic citation: Perry, A., Wachowiak, W., Downing, A., Talbot, R., & Cavers, S. (2020). Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Molecular Ecology Resources, 20(6), 1697-1705.

Pinus sylvestris
type: Concept

Pinus mugo
type: Concept

Pinus uliginosa
type: Concept

Pinus uncinata
type: Concept

conifer
type: Concept

UK Centre for Ecology & Hydrology
type: Organization