University of Oulu

Kastally, C., Niskanen, A. K., Perry, A., Kujala, S. T., Avia, K., Cervantes, S., Haapanen, M., Kesälahti, R., Kumpula, T. A., Mattila, T. M., Ojeda, D. I., Tyrmi, J. S., Wachowiak, W., Cavers, S., Kärkkäinen, K., Savolainen, O., & Pyhäjärvi, T. (2022). Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. The Plant Journal, 109(5), 1337–1350.

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research

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Author: Kastally, Chedly1; Niskanen, Alina K.1; Perry, Annika2;
Organizations: 1Department of Ecology and Genetics, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
2UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, EH26 0QB UK
3Natural Resources Institute Finland (Luke), Paavo Havaksen tie 3, 90570 Oulu, Finland
4Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France
5Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
6Department of Organismal Biology, EBC, Uppsala University, Norbyvägen 18 A, Uppsala, 752 36 Sweden
7Norwegian Institute of Bioeconomy Research, P.O. Box 115, Ås, 1431 Norway
8Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
9Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1 MB)
Persistent link:
Language: English
Published: John Wiley & Sons, 2022
Publish Date: 2022-06-20


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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Series: The plant journal
ISSN: 0960-7412
ISSN-E: 1365-313X
ISSN-L: 0960-7412
Volume: 109
Issue: 5
Pages: 1337 - 1350
DOI: 10.1111/tpj.15628
Type of Publication: A1 Journal article – refereed
Field of Science: 1183 Plant biology, microbiology, virology
Funding: This project received funding from: the European Union’s Horizon 2020 research and innovation program, under grant agreement no. 773383 (to UOULU, Luke and UKCEH); the Seventh framework program for research and development, under grant agreement no. 211868 (to UOULU and Luke); the Academy of Finland, through grants 287431, 293819 and 319313 (to TP), 307582 (to OS), 307581 (to KK) and 309978 (to STK); NoE EVOLTREE and Metsänjalostussäätiö (to STK); and by two grants in the UK, GAPII (NE/K012177/1), funded by Natural Environment Research Council (NERC), and PROTREE (BB/L012243/1), funded jointly by Biotechnology and Biological Sciences Research Council (BBSRC), Department for Environment, Food and Rural Affairs (DEFRA), Economic and Social Research Council (ESRC), the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. The authors wish to thank Joan Beaton and Glenn Iason (James Hutton Institute) for providing Scottish needle samples for genotyping and to acknowledge CSC–IT Center for Science, Finland, for computational resources.
EU Grant Number: (773383) B4EST - Adaptive BREEDING for productive, sustainable and resilient FORESTs under climate change
(211868) NOVELTREE - Novel tree breeding strategies
Academy of Finland Grant Number: 287431
Detailed Information: 287431 (Academy of Finland Funding decision)
293819 (Academy of Finland Funding decision)
319313 (Academy of Finland Funding decision)
307582 (Academy of Finland Funding decision)
Dataset Reference: All relevant data can be found within the article and its supporting materials. Metadata of all SNPs are included in the file Data S1. Genotype data for the 268 samples used in this article are available in .vcf format in the file Data S3, including 10 progenies (135 offspring and their parents) and trees from Finland and Scotland (122 samples).
Copyright information: © 2021 The Authors. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.