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Taming the massive ...
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Kastally, ChedlyUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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2022-01-16
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John Wiley & Sons,2022
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-485715
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-485715URI
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https://doi.org/10.1111/tpj.15628DOI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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.
Subject headings and genre
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Niskanen, Alina K.Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Perry, AnnikaUK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland
(author)
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Kujala, Sonja T.Nat Resources Inst Finland Luke, Paavo Havaksen Tie 3, Oulu 90570, Finland
(author)
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Avia, KomlanUniv Strasbourg, INRAE, SVQV UMR A 1131, F-68000 Colmar, France
(author)
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Cervantes, SandraUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Haapanen, MattiNat Resources Inst Finland Luke, Latokartanonkaari 9, FI-00790 Helsinki, Finland
(author)
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Kesalahti, RobertUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Kumpula, Timo A.Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Mattila, Tiina M.Uppsala universitet,Människans evolution,Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland(Swepub:uu)tiima649
(author)
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Ojeda, Dario, IUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland.;Norwegian Inst Bioecon Res, POB 115, N-1431 As, Norway
(author)
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Tyrmi, Jaakko S.Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Wachowiak, WitoldAdam Mickiewicz Univ, Fac Biol, Inst Environm Biol, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland
(author)
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Cavers, StephenUK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland
(author)
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Karkkainen, KatriNat Resources Inst Finland Luke, Paavo Havaksen Tie 3, Oulu 90570, Finland
(author)
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Savolainen, OutiUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland
(author)
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Pyhajarvi, TanjaUniv Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland.;Univ Helsinki, Dept Forest Sci, POB 27, Helsinki 00014, Finland
(author)
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Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, FinlandUK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland
(creator_code:org_t)
Related titles
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In:The Plant Journal: John Wiley & Sons109:5, s. 1337-13500960-74121365-313X
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Kastally, Chedly
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Niskanen, Alina ...
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Perry, Annika
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Kujala, Sonja T.
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Avia, Komlan
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Cervantes, Sandr ...
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Haapanen, Matti
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Kesalahti, Rober ...
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Kumpula, Timo A.
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Mattila, Tiina M ...
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Ojeda, Dario, I
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Tyrmi, Jaakko S.
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Wachowiak, Witol ...
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Cavers, Stephen
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Karkkainen, Katr ...
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Savolainen, Outi
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Pyhajarvi, Tanja
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