ArticleThe Plant journal : for cell and molecular biology2022
Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 30 citations in OpenAlex.
- Integrating GWAS-guided markers preselection with genomic selection enhances prediction of pulpwood-related traits in slash pine (Pinus elliottii Englem.).BMC plant biology · 2026Article
- The FORGENIUS Genomic Resources: New Genotyping Tools and Genomic Data for 23 Forest Tree Species and Their Genetic Conservation Units.Molecular ecology resources · 2026Article
- Adaptive Potential and Genomic Vulnerability of Keystone Forest Tree Species to Climate Change: A Case Study in Scots Pine.Evolutionary applications · 2025Article
- Needle- and Canopy-Level Genetic Variation in Scots Pine (Evolutionary applications · 2025Article
- Drought Response and Genetic Variation in Scots Pine Seedlings' Provenances: Insights From High-Throughput Phenotyping for Climate-Resilient Forestry.Evolutionary applications · 2025Article
- Low-input breeding potential in stone pine, a multipurpose forest tree with low genome diversity.G3 (Bethesda, Md.) · 2025Article
- Development of a 101.6K liquid-phased probe for GWAS and genomic selection in pine wilt disease-resistance breeding in Masson pine.The plant genome · 2025Article
- Genomic Data Support the Revision of Provenance Regions Delimitation for Scots Pine.Evolutionary applications · 2024Article
- Polymorphic Loci of Adaptively Significant Genes Selection for Determining Nucleotide Polymorphism ofGenes · 2024Article
- Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection inFrontiers in genetics · 2024Article
- A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
17 authors at 8 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called 'PiSy50k'). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.
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