University of Oulu

Baison, J., Vidalis, A., Zhou, L., Chen, Z., Li, Z., Sillanpää, M. J., … García‐Gil, M. R. (2019). Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce. The Plant Journal, 100(1), 83–100.

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)
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Language: English
Published: John Wiley & Sons, 2019
Publish Date: 2019-10-17


Norway 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.

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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
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
112 Statistics and probability
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.