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Genome-wide association study (GWAS) identified candidate loci affecting wood formation in Norway spruce |
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| Author: | Baison, John1; Vidalis, Amaryllis2; Zhou, Linghua1; |
| Organizations: |
1Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Science, Parallellvägen 21, Umeå 907 36, Sweden 2Section of Population Epigenetics and Epigenomics, Centre of Life and Food Sciences Weihenstephan, Technische Universität München, Lichtenbergstr. 2a, München 85748, Germany 3Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
4Department of Mathematical Sciences, Biocenter Oulu, University of Oulu, Pentti Kaiteran katu 1, Oulu, Finland
5Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 4-6, Umeå 907 36, Sweden 6Uppsala Multidisciplinary Centre for Advanced Computational Science, Uppsala University, Lägerhyddsvägen 2, Uppsala752 37, Sweden 7RISE Bioeconomy, Drottning Kristinas väg 61, SE-114 86, Stockholm, Sweden 8Skogforsk, Ekebo 2250, SE-268 90, Svalöv, Sweden 9Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Kåbovägen 4, Uppsala 752 36, Sweden 10IIC, Rosenlundsgatan 48B, SE-118 63, Stockholm, Sweden |
| Format: | article |
| Version: | published version |
| Access: | open |
| Online Access: | PDF Full Text (PDF, 2 MB) |
| Persistent link: | http://urn.fi/urn:nbn:fi-fe2019101733544 |
| Language: | English |
| Published: |
John Wiley & Sons,
2019
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| Publish Date: | 2019-10-17 |
| Description: |
AbstractNorway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome‐wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO‐based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies. see all
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| Series: |
The plant journal |
| ISSN: | 0960-7412 |
| ISSN-E: | 1365-313X |
| ISSN-L: | 0960-7412 |
| Volume: | 100 |
| Issue: | 1 |
| Pages: | 83 - 100 |
| DOI: | 10.1111/tpj.14429 |
| OADOI: | https://oadoi.org/10.1111/tpj.14429 |
| Type of Publication: |
A1 Journal article – refereed |
| Field of Science: |
1181 Ecology, evolutionary biology 1184 Genetics, developmental biology, physiology 112 Statistics and probability |
| Subjects: | |
| Funding: |
All genetic data were obtained through funding from the Knut and Alice Wallenberg foundation. JB is supported though a postdoc position funded by the Kempe foundation. |
| Copyright information: |
© 2019 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. 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. |
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https://creativecommons.org/licenses/by/4.0/ |