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

↓ Direkt till sidans innehåll
↓ Direkt till sidans sekundära innehåll (sidomenyn)

Sökning: WFRF:(Mattila Tiina M.) > Taming the massive ...

LIBRIS Formathandbok (Information om MARC21)

Fältnamn	Indikatorer	Metadata
000		05062naa a2200577 4500
001		oai:DiVA.org:uu-485715
003		SwePub
008		220927s2022 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4857152 URI
024	7	a https://doi.org/10.1111/tpj.156282 DOI
040		a (SwePub)uu
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Kastally, Chedlyu Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
245	1 0	a Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research
264		c 2022-01-16
264	1	b John Wiley & Sons,c 2022
338		a electronic2 rdacarrier
520		a 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.
650	7	a NATURVETENSKAPx Biologix Genetik0 (SwePub)106092 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciencesx Genetics0 (SwePub)106092 hsv//eng
653		a Pinus sylvestris
653		a genotyping
653		a pedigree
653		a single-nucleotide polymorphism
653		a genetic diversity
700	1	a Niskanen, Alina K.u Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Perry, Annikau UK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland4 aut
700	1	a Kujala, Sonja T.u Nat Resources Inst Finland Luke, Paavo Havaksen Tie 3, Oulu 90570, Finland4 aut
700	1	a Avia, Komlanu Univ Strasbourg, INRAE, SVQV UMR A 1131, F-68000 Colmar, France4 aut
700	1	a Cervantes, Sandrau Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Haapanen, Mattiu Nat Resources Inst Finland Luke, Latokartanonkaari 9, FI-00790 Helsinki, Finland4 aut
700	1	a Kesalahti, Robertu Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Kumpula, Timo A.u Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Mattila, Tiina M.u Uppsala universitet,Människans evolution,Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut0 (Swepub:uu)tiima649
700	1	a Ojeda, Dario, Iu Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland.;Norwegian Inst Bioecon Res, POB 115, N-1431 As, Norway4 aut
700	1	a Tyrmi, Jaakko S.u Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Wachowiak, Witoldu Adam Mickiewicz Univ, Fac Biol, Inst Environm Biol, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland4 aut
700	1	a Cavers, Stephenu UK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland4 aut
700	1	a Karkkainen, Katriu Nat Resources Inst Finland Luke, Paavo Havaksen Tie 3, Oulu 90570, Finland4 aut
700	1	a Savolainen, Outiu Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland4 aut
700	1	a Pyhajarvi, Tanjau Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finland.;Univ Helsinki, Dept Forest Sci, POB 27, Helsinki 00014, Finland4 aut
710	2	a Univ Oulu, Dept Ecol & Genet, POB 3000, Oulu 90014, Finlandb UK Ctr Ecol & Hydrol, Bush Estate, Penicuik EH26 0QB, Midlothian, Scotland4 org
773	0	t The Plant Journald : John Wiley & Sonsg 109:5, s. 1337-1350q 109:5<1337-1350x 0960-7412x 1365-313X
856	4	u https://doi.org/10.1111/tpj.15628y Fulltext
856	4	u https://uu.diva-portal.org/smash/get/diva2:1699235/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print
856	4	u https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/tpj.15628
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-485715
856	4 8	u https://doi.org/10.1111/tpj.15628

Hitta via bibliotek

The Plant Journal (Sök värdpublikationen i LIBRIS)

Till lärosätets databas

Hitta mer i SwePub

Av författaren/redakt...: Kastally, Chedly; Niskanen, Alina ...; Perry, Annika; Kujala, Sonja T.; Avia, Komlan; Cervantes, Sandr ...; visa fler...; Haapanen, Matti; Kesalahti, Rober ...; Kumpula, Timo A.; Mattila, Tiina M ...; Ojeda, Dario, I; Tyrmi, Jaakko S.; Wachowiak, Witol ...; Cavers, Stephen; Karkkainen, Katr ...; Savolainen, Outi; Pyhajarvi, Tanja; visa färre...

Om ämnet

NATURVETENSKAP: NATURVETENSKAP; och Biologi; och Genetik

Artiklar i publikationen: The Plant Journa ...

Av lärosätet: Uppsala universitet

Sök utanför SwePub

Sök vidare i:: Google; Google Book Search; Google Scholar

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

LIBRIS.kb.se